saipooja at gmail.com
Wed Jul 21 18:38:40 CEST 2010
Thanks Rodrigo. I have read the paper and and I am familiar with the
This is what I want to do:
I have a version of gromacs without the charmm forcefield which I have
modified to use an algorithm I need.
However, I now need to use charmm ff with this algorithm and in gromacs.
It would be extremely tedious to modify another version of gromacs(with
charmm ff i.e.) for this algorithm. So , I was thinking if I could just copy
the top folder from a git version of gromacs(with charmmff) and make changes
in configure files to make it work with my version?
Can someone give me some pointers on this? For example which files much be
I have some thoughts:
1. Clearly, the topology folder has been changed. It has new files on charmm
and the organization of files has also been changed --> cp topology folder
from git and put into my version
2. Make changes in configure.ac
The git version have extra commands for compiling top files for each
forcefield - copy those commands exactly from the git version and add to my
3. I think that some files connected to pdb2gmx might have to be changed.
Which ones I am not sure. I am only interested in the .c files. Maybe
What else would I need to change? Any pointers would be very helpful. Kindly
let me know even if you have attempted something similar.
On Tue, Jul 20, 2010 at 8:14 PM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:
> The gromacs version in git master, please see the directory
> That directory contains whole gromacs charmm files. Furthermore, please see
> the reference below which explain more details about these parameters.
> Bjelkmar, Larsson, Cuendet, Hess, and Lindahl, JCTC 2010
> I hope those informations help you.
> What do you want to do more specific?
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
> On Tue, Jul 20, 2010 at 6:57 PM, Sai Pooja <saipooja at gmail.com> wrote:
>> If one has to make a version of gromacs charmm compatible, which files
>> from the charmm compatible version must be looked at?
>> Quaerendo Invenietis-Seek and you shall discover.
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Quaerendo Invenietis-Seek and you shall discover.
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