[gmx-users] Is .mdp file are same for each force field?

[jkrieger at mrc-lmb.cam.ac.uk]

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
James

> 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, md.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 field
> 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 to
> 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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