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Setup, I/O, and Basic questions Jump to new posts
Re: Missing donor specification in RTF Ripplet 09/28/20 01:21 AM
Thank you so much. I understand now.
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Setup, I/O, and Basic questions Jump to new posts
Re: Missing donor specification in RTF rmv 09/27/20 06:05 PM
For this atom, you can use either SELE TYPE HN END or SELE CHEM H END; note that other hydrogens besides the backbone amide HN also correspond to CHEM H, such as protons on side chain NH2 or OH. The selection TYPE HN is more specific, while CHEM H is more general as it can be used for other atom TYPEs.
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Setup, I/O, and Basic questions Jump to new posts
Re: Missing donor specification in RTF Ripplet 09/27/20 11:30 AM
Thank you very much!
For the second question, I still feel confused. For example, I saw there are type H for hydrogens in Cys secification as following, the type of the hydrogen connected to nitrogen is H, but when I use "select type H end", I could not select any atom.

RESI CYS 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
4 31 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Missing donor specification in RTF lennart 09/27/20 08:18 AM
DONOR/ACCEPTOR ADD (hbonds.info)
The TYPE is the name of the atom in the RTF, whereas the chemical identiry of the atom is referred to as CHEM.
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Setup, I/O, and Basic questions Jump to new posts
Missing donor specification in RTF Ripplet 09/27/20 08:11 AM
Dear all,
First question: If the donor specification in RTF is missing, can we add them in an anlysis fileļ¼Ÿ If yes, how?
Second question: I found there are type H in the RTF file, while when I used "select type H end" and got the result of "0 atom has been selected"?
Thank you very much for your kind help.
Best Wishes,
Ripplet
4 31 Read More
Other User Discussion and Questions Jump to new posts
No velocity inversion at lower boundary with AXD module cm14sjm 09/24/20 12:41 PM
Hi

I've been doing some production runs using the AXD module in charmm which have been running for some time without crashing with errors etc. But when I've gone to look at the progress of the runs through the axd files I have large sections where the trajectory hasn't been inverted when it hits the lower boundary and so it keeps going back on itself rather than being forced to carry on until the end boundary I've set.

An example is found at the bottom of the attached and file where the trajectory has gone from around 48 to 45A when there should be boundaries every 0.5A and so it should be confined by the boundary at 48A. I've attached the corresponding input file with the AXD command in too.

Thank you
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Setup, I/O, and Basic questions Jump to new posts
Re: Running charmm36+CMAP with FACTS lennart 09/17/20 04:40 PM
I don't think I can test it, but when you ask a question you should always upload a clean, brief and complete inputfile, and the resulting logfile. AND please always state which CHARMM version you are using.
3 68 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Running charmm36+CMAP with FACTS pmj 09/16/20 04:11 AM
Dear Lennart,

thank you for your answer.

It is written FACTS was parallelized in 2007., and I tried to run it with the serial version of charmm, but I get the same error.

Would it be okay if I attach my files for you to test it?

Best
Paula
3 68 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Running charmm36+CMAP with FACTS lennart 09/15/20 08:48 PM
FACTS is an implicit solvent model, so it makes more sense to use it with the parameter set for which it was developed.
The problem you report may be due to your trying to run this in parallel, which may not be supported.
3 68 Read More
Setup, I/O, and Basic questions Jump to new posts
Running charmm36+CMAP with FACTS pmj 09/15/20 08:05 PM
Hi!

I would like to use charmm36 with CMAP instead of charmm22 with FACTS.

I have both nucleic acids and protein in my system.

It is written that there are only two choices:

TCPS 22 Choice of force field: all-atom (22) or polar hydrogens,
i.e., extended carbon and sulfur atoms (19).
Note that TCPS 22 also works
with param27, although only protein atoms are parameterized.

I added the following in my script:

set diele 1.0

nbond nbxmod 5 atom cdiel eps @diele shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 e14fac 1.0 wmin 1.5

scalar wmain = radius

facts tcps 22 teps @diele gamm 0.015 TAVW


If I use the upper commands the simulation begins but there is one single line being repeated endlessly as in the attached photo.


If someone can just help me with the setting it up, I would appreciate it.

Thanks
Paula
3 68 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: IC edit usage aroman 09/15/20 02:33 AM
Sry for late reply.
I solved this problem. I stupidly used old CHARMM, c35 version. The newest CHARMM is working fine.
2 75 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: IC edit usage rmv 09/09/20 02:25 PM
What is the CHARMM version?

Can you use COOR PRINT to show the coordinates for those atoms?
2 75 Read More
Installation and Testing Jump to new posts
Re: Problem Compiling C45b1 - Free Version milan 09/09/20 08:08 AM
gcc-10 is not working with CHARMM, unless you compile without optimization (-O2)

it would be helpful to reduce the level of optimization just for few files during the CHARMM compilation to ease the debugging. For now just use gcc-9.3, for example.

Milan
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Installation and Testing Jump to new posts
Re: cmake for charmm lennart 09/09/20 07:03 AM
So with cmake you would do this:
mkdir gnu_m
cd gnu_m
../configure
make
cd ..
mkdir gnu
cd gnu
../configure --without-mpi
make
3 91 Read More
Setup, I/O, and Basic questions Jump to new posts
IC edit usage aroman 09/09/20 06:18 AM
Dear all,
I have a question about using IC edit.
My protein structure has residues over 1000. I edited some dihedrals in the residues having residue number beyond 1000 like the following.

Code
IC edit  
dihe pro0 1000 N pro0 1000 CA pro0 1000 CB pro0 1000 OG 60.0
end

The residues below 1000 (3 digits) were all ok but they failed to read with the error:

Code
*****  WARNING  ***** GETATN could not find the RESIDUE SEG="PRO0" RES="1000" ATOM="N   "
 *****  WARNING  ***** GETATN could not find the RESIDUE SEG="PRO0" RES="1000" ATOM="CA  "
 *****  WARNING  ***** GETATN could not find the RESIDUE SEG="PRO0" RES="1000" ATOM="CB  "
 *****  WARNING  ***** GETATN could not find the RESIDUE SEG="PRO0" RES="1000" ATOM="OG  "

Could u help me solve this problem?
Thanks alot
2 75 Read More
Installation and Testing Jump to new posts
Re: cmake for charmm rossi 09/08/20 09:16 PM
Hello,

Thank you for your response.

I always use the serial version first when developing a new project, but I suppose that is a matter of procedure.

Your question about how to make to two versions is exactly my point.

The old method of compiling yields for me:

/home/rossi/Downloads/workshop/charmm/c42b1/exec/gnu_M/charmm ---> parallel version
/home/rossi/Downloads/workshop/charmm/c42b1/exec/gnu/charmm ---> serial version

and compiling is performed easily with just one switch change.

I would like to add the following to my original post:

4. www.charmm.org ----> Documentation ---> installation

Most of the content under installation refers to the old manner of compiling. Perhaps, it might be better to remove that material, and add the new information for cmake.

Warm regards,

Angelo
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Installation and Testing Jump to new posts
Re: cmake for charmm lennart 09/08/20 06:34 PM
Try configure --help to get more information about controlling the build procedure.
I never bother with the serial version, except for testing; the only time it is needed, as far as I know, is if you want to run it on a machine which does not have the same parallel environment as the machine used for the build.
How do you use the cmake build procedure to build different versions in the same build directory (eg, serial and parallel, or with any of a large number of other options), other than actually doing "../configure, make" in the same directory - in which case you could not reasonably expect the outcome to be anything else than an executable named "charmm"?
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Installation and Testing Jump to new posts
cmake for charmm rossi 09/06/20 09:11 PM
Hello,

The installation information (cmake.info) could use more information and perhaps some changes:

1. The name of the executable is the same for both the serial and parallel versions leading to possible confusion. Unless two different build directories are used for the cmake, one executable will be overwritten by the second.
2. In my opinion, the serial version should be the default for compilation. The serial version is the one I use for both testing and development of a project. Later, I would move to the parallel version either on my laptop or to the university cluster. I think this is the most logical way to proceed.
3. The following is partial output from the old install.com script


Q replace QUANTUM with GAMESS.
U replace QUANTUM with GAMESS-UK.
C replace QUANTUM with CADPAC.
T replace QUANTUM with SCCDFTB.
QC replace QUANTUM with Q-CHEM.
QT replace QUANTUM with Turbomole.
SQ replace QUANTUM with SQUANTUM, only with altix/gnu.
W replace QUANTUM with MNDO97, only with altix/gnu.
QS replace QUANTUM with QMMMSEMI (AMBER Semi-empirical QMMM).
G09 replace QUANTUM with Gaussian09.
APBS compile with APBS support.
FFTW compile with FFTW support (adds COLFFT keyword to pref.dat).
MKL compile with MKL support (adds COLFFT keyword to pref.dat).
OPENMM add support for OpenMM (see openmm.doc)
PIPF add support for Polarizable Intermolecular Potential Function
POLYR add support for POLYRATE interface
GAMUS add support for GAMUS (requires LAPACK installation)

but the cmake.info doesn't indicate how the new procedure will handle these options, or will not handle these options, or perhaps it doesn't matter.

Is it possible to say something about how the options above are handled with cmake?

Regards,

Angelo
3 91 Read More
Installation and Testing Jump to new posts
Problem Compiling C45b1 - Free Version rossi 09/06/20 08:49 PM
Hello,

I am hoping that someone can provide direction on the following problem.

./charmm -i h2o-graphene-styr-heat.inp -o h2o-graphene-styr-heat.log&

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x150079847bd0 in ???
#1 0x150079846e25 in ???
#2 0x1500794fee2f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
#3 0x55a89bce2710 in ???
#4 0x55a89b794139 in ???
#5 0x55a89b4d6ff4 in ???
#6 0x55a89b4d8d72 in ???
#7 0x55a89b4d5bde in ???
#8 0x1500794e9cc9 in __libc_start_main
at ../csu/libc-start.c:308
#9 0x55a89b4d5c39 in ???

I have downloaded the free version of charrm C45b1, from the charmm website.

This is the operating system on my local laptop:
Sun Sep 06 16:33:28 [rossi@debian ~]$uname -a
Linux debian 5.7.0-3-amd64 #1 SMP Debian 5.7.17-1 (2020-08-23) x86_64 GNU/Linux

This is the gnu compiler version on my local laptop.
Sun Sep 06 16:33:34 [rossi@debian ~]$gcc -dumpversion
10 or version 10.2.0

The same error above occurs with the parallel version on my laptop, and
both exercutables were compiled with cmake.

Here is the gnu compiler version on the UConn cluster:
[anr11010@cn02 misc]$gcc -dumpversion
5.4.0

The same input above file works with a parallel version of charmm C45b1 on the UConn Linux cluster.

I understand that my laptop has a very new version of the compiler, but has charmm been tested with the latest and greatest versions of the gnu compiler?

Any help, direction, hints, and ideas would be extremely helpful.

Thanks so much for your attention to this.

Kind regards,

Angelo
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