Previous Thread
Next Thread
Print Thread
Running charmm36+CMAP with FACTS
#38082 09/15/20 08:05 PM
Joined: Jan 2019
Posts: 58
P
pmj Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Jan 2019
Posts: 58
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

Attached Files
Screenshot 2020-09-15 at 22.02.31.png (888.58 KB, 15 downloads)
Re: Running charmm36+CMAP with FACTS
pmj #38083 09/15/20 08:48 PM
Joined: Sep 2003
Posts: 4,797
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,797
Likes: 2
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Running charmm36+CMAP with FACTS
lennart #38084 09/16/20 04:11 AM
Joined: Jan 2019
Posts: 58
P
pmj Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Jan 2019
Posts: 58
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

Re: Running charmm36+CMAP with FACTS
pmj #38085 09/17/20 04:40 PM
Joined: Sep 2003
Posts: 4,797
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,797
Likes: 2
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  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: 0.007s Queries: 23 (0.004s) Memory: 0.9132 MB (Peak: 0.9968 MB) Data Comp: Off Server Time: 2020-10-29 08:04:28 UTC
Valid HTML 5 and Valid CSS