[gmx-users] proper mdp options

[Anton Feenstra]

Lukas wrote:
> 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
> interactions?

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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