RE: Included Topology (.itp) in gromacs to parameter file for NAMD

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jul 03 2018 - 11:51:12 CDT

Hi Ivan,

How is this fed into GROMACS? Is the .xvg fed in during the generation of the .top file, or is it a parameter to mdrun? NAMD should be able to read in a GROMACS .top file (see http://www.ks.uiuc.edu/Research/namd/2.12/ug/node14.html) if it is the first option, with the caveat that NAMD doesn't parse "#include" statements in a .top file, but not if it is the second.

-Josh

On 2018-07-03 02:46:48-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Thank you very much for all the work you do and keeping the NAMD project alive.
I've recently seen an article about a customized force field for GROMACS with an .itp extension and a .xvg tabulated table for the dihedral interactions. I would like to convert that to use it on NAMD and continue to make accurate simulations using NAMD, so it has to have AMBER or CHARMM format I guess.
I've searched the internet and on this site I found this:
"... the Gromacs force field uses a different type of function
(for proper and improper dihedrals) than the Charmm force field. Gromacs
appears to use harmonic and periodic functions while Charmm uses modified
Fourier series. "
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2004-2005/0968.html%7Cf9b7ce58097847667c6408d5e0c180df%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636662044069868686&sdata=yygV8kAqLOTJjN5xRCbYQ6rNl5x%2FCFHgsIt2oH8xyFQ%3D&reserved=0>
How can I solve this? Any idea? Is this even possible to do?
Thank you in advance,
Ivan

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