AW: Running gromacs in namd

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Dec 01 2016 - 01:06:23 CST

 

Can you explain in short what changed you had to made, just to have this here for users having these issues in the future.

 

Norman Geist

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Subbarao Kanchi
Gesendet: Donnerstag, 1. Dezember 2016 07:28
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Running gromacs in namd

 

Hi Norman Geist,

                         Thank you for the suggestions and I have modified the gromacs topology file by looking at the namd source code "GromacsTopFile.C". It is working.

Thanks,

Subbarao Kanchi.

 

On Wed, Nov 30, 2016 at 2:15 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

Have you tried sending your topology through one of the gromacs tools to check it is correct? Otherwise, since gromacs support in namd is rather rudimentary, you could also try to convert your gromacs files to amber format using the Parmed tool, either directly downloaded from github or shipped with the Ambertools 16, as:

 

parmed

parmed> gromber your.top your.gro

parmed> outparm your.prmtop your.rst7

 

It might also output errors your topology has issues. Later in namd you do;

 

amber on

parmfile your.prmtop

ambercoor your.rst7

 

Best wishes

 

Norman Geist

 

Von: Subbarao Kanchi [mailto:ksubbu85_at_gmail.com <mailto:ksubbu85_at_gmail.com> ]
Gesendet: Dienstag, 29. November 2016 11:25
An: Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >
Cc: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Betreff: Re: namd-l: Running gromacs in namd

 

Hi Norman Geist,

                        I have copied the *.itp into the topologies file (.top) and end up with another error "Syntax error in ATOMS" as reported in mailing list http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/1102.html. I do not find any solution to overcome the error.

Thanks

Subbarao Kanchi

 

On Tue, Nov 29, 2016 at 1:06 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

Well, the exact error is just:

 

Molecule DMPC undefined

 

This is because namd doesn’t follow linked *.itp files from your topology file. Please just copy the content of all required *.itp files into your *.top file and try again.

 

Best of luck

 

Norman Geist

Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von Subbarao Kanchi
Gesendet: Dienstag, 29. November 2016 07:31
An: mmakowsk_at_uci.edu <mailto:mmakowsk_at_uci.edu>
Cc: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Betreff: namd-l: Running gromacs in namd

 

Dear Michael Makowski,

                                   I am trying to run gromacs simulation in namd and getting the error "USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Molecule DMPC undefined" I have seen your post in the mailing list "http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/1129.html". Could you let me know that how did you overcome this problem to run gromacs simulation in namd.

Thanks,

Subbarao Kanchi.

 

 

 

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