[gmx-users] proper mdp options
feenstra at chem.vu.nl
Thu Apr 17 10:14:01 CEST 2003
> Hi all,
> I'm doing a simulation on a small protein. The protein is very unstabel in the
>simulation and the rmsd after ~ 40 ns is already 0.6 nm for the backbone atoms.
> I am using the gromos force field.
> This really makes me wonder if any of the mdp-parameters is very wrong cause the
> temperature is really low. Probably there is something wrong with the non-bonded
In terms of atom mobility, 278K is *not* very low. Kinetic energies are still
at same order as at 300K. I'd not suspect the interactions, but rather the
starting structure. Then, also, 40 ns is not a short time.
How small is your protein.
> here are the mdp-options:
> nstlist = 5
> ns_type = grid
> rlist = 0.8
> ;# non bonded interactions
> coulombtype = Reaction-Field
> epsilon_r = 54
> rcoulomb = 1.4
> vdwtype = cut-off
> rvdw = 0.8
Why not put rvdw at 1.4 also? I think that is the preferred setting
for the Gromos ff's.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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