[gmx-users] Simulation in vaccum
Mark.Abraham at anu.edu.au
Wed Nov 22 05:20:10 CET 2006
nur avneet wrote:
> Dear ALL
> when we simulate in vaccum, first we do steepest descent, then conj,
> then md in vac.
> I want to know that, Do we use periodic boundary conditions here..
That depends if you want an isolated system in vacuo, or a periodic
system in vacuo.
> also if we dont specify anything about pbc in mdp file wht does gromacs
> take it as...
Don't know, but if you try grompp without pbc set, then the file that is
output by the -po flag (default grompp.mdp) will tell you what value was
used - i.e. the default value.
> Also please tell me, is their any particular value of emtol in mdp files
> of steep and cg, that we should use... I use emtol=1000 in the steep
> file, and then when i do cg i keep it 100, 50, 10, 8, 2 step by step.
The emtol value is probably fine, but I suspect your cg regime is a
little vigorous for preparing for MD. If you were about to do a normal
mode analysis, then that would be different...
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