[gmx-users] Is .mdp file are same for each force field?
cbb.chintan at gmail.com
Sun Feb 12 19:00:31 CET 2017
Thanks James for your valuable reply
On Feb 12, 2017 10:06 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
> Hi Chintan,
> 1. No, all forcefields have different parameters that you need to take
> into account in your .mdp files, especially non-bonded cut-offs such as
> rlist and rvdw, which are an integral part of the forcefield. Certainly
> you need to use a forcefield that includes zinc if you have zinc in your
> protein (that said the error could also be that zinc is present but not be
> called ZN in some forcefields). You can get bits of mdp files that are
> forcefield-specific on the gromacs website e.g.
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM - you
> can remove the /CHARMM and get a page to click through others.
> 2. Any mdp with constant temperature would need changing i.e. nvt.mdp,
> npt.mdp and md.mdp - you should really read through the mdp files and
> understand what's going on. Also look at
> http://manual.gromacs.org/online/mdp_opt.html and there are options
> related to temperature coupling. You may want to equilibrate to higher
> temperature in steps by copying nvt.mdp and changing each one to have
> progressively higher values.
> Best wishes
> > Dear gromacs user,
> > I practiced of MD stimulation with LysoZyme tutorial. Now, They used 15:
> > OPLS-AA/L force field and also i saved all *.mdp* file (ions. mdp,
> > nvt.mdp, npt.mdp, minim.mdp, etc.) as given in tutorial and successfully
> > performed MD stimulation.
> > Now, I have want to study my protein. I found force field 9 to 14 are
> > reported for my protein in literature. Further, I also tried it and found
> > "Residue 'ZN' not found in residue topology database" only for force
> > 15 (OPLS-AA/L force field), not for any other force field (9 to 14).
> > *Now, I have two questions.*
> > *1) Can i use this file for stimulation study with other force field (9
> > 14)? If not, from where i get them?*
> > *2) Also want to study MD at higher temperature, still Can i use tutorial
> > .mdp files? or what informations i have to change in files (.mdp)*
> > Can any one tell me what to do?
> > --
> > Regards,
> > Chintan Bhagat
> > Research scholar,
> > V.N.S.G.U, India
> > --
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