Re: [gmx-users] how to simulate a line charge

I change the maximum charge group size defined in the include/types/nblist.h header from 32 to 267. Then grompp worked fine but the mdrun did not start. The following error came out Program mdrun_jptlc, VERSION 4.5.3 Source code file: ns.c, line: 2417 Fatal error: Max #atoms in a charge group:

[gmx-users] Regarding g_sham

Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- ---

[gmx-users] do_dssp

Hi, I'm trying to use do_dssp of gromacs 4.5.4 in fedora core . I did processes of Download , Uncompress and Compile the source code as the following unzip dsspcmbi.zip cd dssp [root@localhost dssp]# ./DsspCompileGCC That i got this message: Running script to compile the CMBI version of

Re: [gmx-users] Regarding g_sham

On Sat, Aug 13, 2011 at 3:36 PM, bipin singh bipinel...@gmail.com wrote: Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the

[gmx-users] aldehida

Dear all, I want simulate a aldehida group near CNT. my aldehida has benzene as functional group(-R). My first question is about suitable force field to simulation of  aldehida.What kind of force field you suggest?  And also I know that one of the important force between CNT and

Re: [gmx-users] Regarding g_sham

Thanks for yor reply... I have read manual but there is no description available for the -map -ls3 -mdata options of g_sham On Sat, Aug 13, 2011 at 15:56, lina lina.lastn...@gmail.com wrote: On Sat, Aug 13, 2011 at 3:36 PM, bipin singh bipinel...@gmail.com wrote: Hello, Please let me know from

Re: [gmx-users] how to simulate a line charge

Amit Choubey wrote: I change the maximum charge group size defined in the include/types/nblist.h header from 32 to 267. Then grompp worked fine but the mdrun did not start. The following error came out Program mdrun_jptlc, VERSION 4.5.3 Source code file: ns.c, line: 2417 Fatal error: Max

Re: [gmx-users] do_dssp

afsaneh maleki wrote: Hi, I'm trying to use do_dssp of gromacs 4.5.4 in fedora core . I did processes of Download , Uncompress and Compile the source code as the following unzip dsspcmbi.zip cd dssp [root@localhost dssp]# ./DsspCompileGCC That i got this message: Running script to

Re: [gmx-users] aldehida

hamed amini wrote: Dear all, I want simulate a aldehida group near CNT. my aldehida has benzene as functional group(-R). My first question is about suitable force field to simulation of aldehida.What kind of force field you suggest? And also Many could be used. Probably the only ones

Re: [gmx-users] aldehida

hamed amini wrote: Dear Lemkul, thank you very much for your quick respond. But what parameters is involved in selection of force field? Is CHARMm27 selection good? You should choose a force field based on whether or not it can accurately describe the molecule(s) you're interested in

Re: [gmx-users] How to suppress the screen info how to overwrite files?

On Fri, Aug 12, 2011 at 19:23, Justin A. Lemkul jalem...@vt.edu wrote: Try setting the environment variable GMX_MAXBACKUP to zero. This environment variable is read only by the 4.5 series. In 4.0.7 there is no way to control it, there is a hard-coded limit of 128. Cheers, Bogdan -- gmx-users

Re: [gmx-users] how to simulate a line charge

On Sat, Aug 13, 2011 at 05:43, Amit Choubey kgp.a...@gmail.com wrote: The largest charge group contains 267 atoms. The maximum is 32. Column 6 in the [atoms] section of the .top file defines the charge group. If you want each atom to be in its own charge group, you can set this to the same

Re: [gmx-users] how to simulate a line charge

Thanks Bogdan, defining each atom as a charge group solves the grompp issue. Also here the atoms interact via non-bonded potentials. I think its a better way to simulate the line charge. Amit On Sat, Aug 13, 2011 at 8:29 AM, Bogdan Costescu bcoste...@gmail.comwrote: On Sat, Aug 13, 2011 at

Re: [gmx-users] how to simulate a line charge

I was not sure if changing the size of maxcg would not negatively influence anything else. I will give it a try. Thanks Justin On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: I change the maximum charge group size defined in the