Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
Termination in equilbrium when heating
#37931 06/14/20 03:11 AM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Hello all,

Today I have a question about my solvation. After immersing in a droplet of water, I try to equilbrium, but there is a abnormal termination when heating. This is the code:

DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA MISCEL: SBOUnd TSM PRMS PANGle other
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
---------- --------- --------- --------- --------- ---------
DYNA> 0 0.00000-299487.95558 0.00000-299487.95558 0.00000
DYNA PROP> 28.72222-299327.78729 480.50490 160.16830 -13858.10193
DYNA INTERN> 0.00000 922.19829 207.86836 1105.91786 46.22287
DYNA EXTERN> 10501.32156-312122.45716 0.00000 0.00000 0.00000
DYNA MISCEL> -149.02736 0.00000 0.00000 0.00000 0.00000
DYNA PRESS> 210133.59958-200894.86496 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
UPDECI: Nonbond update at step 1
UPDECI: Nonbond update at step 6
UPDECI: Nonbond update at step 10
UPDECI: Nonbond update at step 13
UPDECI: Nonbond update at step 14
WRIDYN: RESTart file was written at step 15


Writing RESTART FILE with previous and current coordinates,
which may be read by: READ COOR DYNR .... (see io.doc).
NOTE!! THIS FILE C A N N O T BE USED TO RESTART A RUN!!!



***** LEVEL -2 WARNING FROM *****
***** ENERGY CHANGE TOLERANCE EXCEEDED
******************************************
BOMLEV ( -1) IS REACHED - TERMINATING. WRNLEV IS 0

ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -2

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 20.79 MINUTES
CPU TIME: 20.70 MINUTES


So how can I deal with it?
help would be greatly appreciated
wenhao

Re: Termination in equilbrium when heating
dengwenhao #37932 06/14/20 05:27 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,532
Likes: 2
One possibility is that the structure has not been adequately minimized after solvation. There could also be some issues with your dynamics input script. One thing to note is that the last error or warning message may be a symptom of an earlier problem.


Rick Venable
computational chemist

Re: Termination in equilbrium when heating
rmv #37933 06/15/20 09:51 AM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Thank you so much. Now I still try my best to deal with this problem. But I dont know what is your meaning about "an earlier problem"? To be honest,after my first minimization, the first residue and the final resdue were abnormal(bonding of unrelated atoms that needn‘t bond). But I used an order:define heavy sele all .and. .not. ( bynu 1:28 .or. bynu 12547:12569 .or. resname TIP3 .or. hydrogen) end.Then the minimization was fine and the mini file were used as input file for solvation.

Re: Termination in equilbrium when heating
dengwenhao #37934 06/15/20 03:28 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,532
Likes: 2
That makes no sense; once a proper PSF is created, atoms are either bonded to each other or they are not, and minimization cannot change that.

As for an earlier problem, the answer can often be found by careful reading of the output log files from CHARMM.

You've posted so little useful information that we can only guess.


Rick Venable
computational chemist

Re: Termination in equilbrium when heating
rmv #37935 06/16/20 08:09 AM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Thank you very much ,really. I should tell you about the step of minimization : the out PSF file of minimization before solvation is normal(displaying no bond), but when I open the out PDB-minimization using VMD,the image is abnormal for the first residue and last residue. So my teacher told me to use the order. I will cannot deal with the abnormal bonds without the order, sorry, I am a new learner for Charmm.
I really thank you for your reply and your time.There are log files in the attachment. Thank you again and wish you happy every day.

Attached Files
log-files.zip (293.52 KB, 99 downloads)
SHA1: cc5f58956731b3964f509d835e55aad6178f7e58
Re: Termination in equilbrium when heating
dengwenhao #37936 06/16/20 05:04 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,532
Likes: 2
VMD will not display bonds correctly unless you read a PSF before coordinates; for CHARMM, using the COOR file (VMD .cor) is recommended, using PDB is not


Rick Venable
computational chemist

Re: Termination in equilbrium when heating
dengwenhao #37937 06/16/20 06:10 PM
Joined: Sep 2003
Posts: 4,810
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,810
Likes: 2
Input files are also quite informative, and a lot easier to read than lengthy log files. You should strive to post a very brief input file (and the corresponding log file) that shows the alleged bad behavior.
Do not use wrnlev, prnlev or bomlev commands.
Your logfiles are so cluttered with mostly uninteresting information that they are unreadable.
A "define" command does not in itself do anything.
The PSF is not changed by coordinate manipulations such as minimization.
And please always use the most recent version of CHARMM.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Termination in equilbrium when heating
rmv #37938 06/20/20 02:33 AM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Yes,teacher. I definitely used the COOR file for Charmm. I really cannot deal with this abnormal termination, even if I change the inp file for equilbrium:shake bonh tolerance 1.0e-6 parameter (change the number). How can I do next?

Re: Termination in equilbrium when heating
lennart #37939 06/20/20 02:45 AM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Thank you for your reply and suggestions. I still cannot deal with this complicated termination in heating 300K. There are input files and corresponding log files in the attachment. Thank you again and wish you happy every day.

Attached Files
inp and log.zip (297.26 KB, 87 downloads)
SHA1: 41518e4bb2301eb3fdb2d88a30859a3a9a062d27
Re: Termination in equilbrium when heating
dengwenhao #37940 06/20/20 04:50 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,532
Likes: 2
Please stop using PRNLEV 10 (or 15) for these output logs if you want us to look through them; use the default (PRNLEV 5), or PRNLEV 6 at most.

The CHARMM version is several years out of date.

You also appear to be using out of date, modified parameters, which could be one of the many problems in this set of files. The extraneous character warning indicates an issue with how the file edited at some point. You should resolve the errors that occur during parameter reading.

Code
CHARMM>    ! Parameter files
 CHARMM>    open read unit 2 card name /home/dengwenhao/5ymr/par_all_isethionate.prm
 VOPEN> Attempting to open::/home/dengwenhao/5ymr/par_all_isethionate.prm::
 OPNLGU> Unit  2 opened for READONLY access to /home/dengwenhao/5ymr/par_all_isethionate.prm
  
 CHARMM>    read para card unit 2

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> *>>>>>> COMBINED CHARMM ALL-HYDROGEN PARAMETER FILE FOR <<<<<<<<<
 TITLE> *>>>>>>> CHARMM22 PROTEINS AND CHARMM27 NUCLEIC ACIDS <<<<<<<<<<
 TITLE> *FROM
 TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<
 TITLE> *>>>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<
 TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<
 TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU  <<<<<<<<<
 TITLE> *AND
 TITLE> *  \\\\ CHARMM27 ALL-HYDROGEN NUCLEIC ACID PARAMETER FILE ////
 TITLE> *  \\\\\\\\\\\\\\\\\\ DEVELOPMENTAL ////////////////////////
 TITLE> *       ALEXANDER D. MACKERELL JR. AND NICOLAS FOLOPPE
 TITLE> *                       AUGUST 1999
 TITLE> *    ALL COMMENTS TO ADM JR.  EMAIL: ALEX,MMIRIS.AB.UMD.EDU
 TITLE> *            TELEPHONE: 410-706-7442
 TITLE> *
 **** Warning ****  The following extraneous characters
 were found while command processing in PARRDR
 £°
 PARRDR> WARNING: ATOM FOR NBOND OSL  DOESNT EXIST
PARRDR> ALL ANGLES HAVE POSITIVE MINIMA
 PARRDR> Error: Repeated BOND parameter ( 19992): SF    FE  
 PARRDR> Error: Repeated BOND parameter ( 14901): ON2   CT2 
 PARRDR> Error: Repeated BOND parameter ( 11579): NN2   HN2 
 PARRDR> Error: Repeated BOND parameter (  4269): FE    SS  
 PARRDR> Error: Repeated BOND parameter (  4246): FE    NPH 
 PARRDR> Error: Repeated BOND parameter (  4238): FE    NR2 
 PARRDR> Error: Repeated BOND parameter (  4223): FE    CM  
 PARRDR> Error: Repeated BOND parameter (  4222): FE    CPM 

The initial minimization energies indicate possible issues with the model building; very high VDW energy. You should also be using SHAKE BONH PARAM at this point, and with the default 1.e-9 tolerance; the same applies to the post-solvation minimization.

Why are you using CONS FIX for all the heavy atoms? This is highly inadvisable, and means you aren't really doing much minimization.

This is a good example of the wrong way to condition an initial model to prepare it for dynamics.


Rick Venable
computational chemist

Re: Termination in equilbrium when heating
rmv #37942 06/21/20 02:15 PM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Thanks,my teacher. Thank you for your suggestions and your time. And this time I tried again and again.

I used SHAKE BONH PARAM at initial minimization before solvation, but I found the energy was higher than previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9 ). So which one is better?

Previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 3311-238148.54483 -0.00000 0.00000 0.00000
ABNR INTERN> 370.48897 984.70990 200.06852 1085.15295 53.42740
ABNR EXTERN> -182.76891-240659.62365 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

Now( using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 10000-237452.82606 -0.00000 0.00000 0.00000
ABNR INTERN> 13.44942 1160.91816 244.89701 1091.79712 53.47728
ABNR EXTERN> 172.68940-240190.05445 0.00000 0.00000 0.00000


When I used SHAKE BONH PARAM at the post-solvation minimization( set the number 1.0e-9, not previously1.0e-6), the abnormal termination still happened. I felt disappointed very much.I just want to try again and I deleted "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" in inp for equilbirum, then it worked and the abnormal termination didn't happen. So I want to ask: Can I delete this script "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" ? I am afraid for this action. Is this deleting operation harmful for next steps?

Thank you again for your time, my teacher, thank you!

Re: Termination in equilbrium when heating
rmv #37943 06/21/20 02:15 PM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Thanks,my teacher. Thank you for your suggestions and your time. And this time I tried again and again.

I used SHAKE BONH PARAM at initial minimization before solvation, but I found the energy was higher than previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9 ). So which one is better?

Previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 3311-238148.54483 -0.00000 0.00000 0.00000
ABNR INTERN> 370.48897 984.70990 200.06852 1085.15295 53.42740
ABNR EXTERN> -182.76891-240659.62365 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

Now( using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 10000-237452.82606 -0.00000 0.00000 0.00000
ABNR INTERN> 13.44942 1160.91816 244.89701 1091.79712 53.47728
ABNR EXTERN> 172.68940-240190.05445 0.00000 0.00000 0.00000


When I used SHAKE BONH PARAM at the post-solvation minimization( set the number 1.0e-9, not previously1.0e-6), the abnormal termination still happened. I felt disappointed very much.I just want to try again and I deleted "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" in inp for equilbirum, then it worked and the abnormal termination didn't happen. So I want to ask: Can I delete this script "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" ? I am afraid for this action. Is this deleting operation harmful for next steps?

Thank you again for your time, my teacher, thank you!

Re: Termination in equilbrium when heating
dengwenhao #37945 06/21/20 05:15 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,532
Likes: 2
You must use SHAKE BONH PARAM throughout; the errors are caused by other problems, such as the use of CONS FIX instead of harmonic restraints, a possibly corrupted parameter file, and maybe an initial model that isn't very good.

Verify the parameter file, perhaps using a simpler model.

Revise the minimizations to use CONS HARM instead of CONS FIX, and do not apply it to all heavy atoms; just the backbone atoms is likely a better choice. The best choices depend on the source of the model; I would treat a crystal structure differently that one constructed from a software package.


Rick Venable
computational chemist

Re: Termination in equilbrium when heating
rmv #37946 06/22/20 01:46 AM
Joined: Jun 2020
Posts: 14
D
Forum Member
OP Offline
Forum Member
D
Joined: Jun 2020
Posts: 14
Ok,thanks. Though I don't know the reason why we must use SHAKE BONH PARAM throughout, but I believe you are right. At the same time, maybe I know where I should change, I almost forget ask : how do I change the script to achieve the purpose of applying "CONS HARM"(your suggestion) to the backbone atoms instead of all heavy atoms.

This is my old script:
!Make sure no constrains exist
cons fix sele none end

define heavy sele all .and. .not. ( resname TIP3 .or. hydrogen) show end

!Constrain needed locations
cons fix sele heavy end

How do I change my old script, my teacher?

Thank you again for your valuable suggestions. Thank you!

Re: Termination in equilbrium when heating
dengwenhao #37947 06/22/20 02:47 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,532
Likes: 2
The CHARMM force field was designed and tested using the SHAKE BONH constraint. The water model in particular is rigid, and requires SHAKE to keep it that way. The PARAM keyword ensures that X-H bonds are constrained to their parameter set values.

Please read the documentation (cons), and look at some the posts in the Script Archive to get some idea of how this is supposed to be done.

Using CONS FIX on all heavy atoms and leaving only the H atoms free to move is an extremely bad idea, indicating either you have received very bad advice, or have not done the proper amount of study yourself before attempting to use this complex program. Make some effort, and show that you have done so.


Rick Venable
computational chemist

Page 1 of 2 1 2

Moderated by  BRBrooks, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.030s Queries: 46 (0.018s) Memory: 1.0442 MB (Peak: 1.2185 MB) Data Comp: Off Server Time: 2021-02-28 00:36:44 UTC
Valid HTML 5 and Valid CSS