[gmx-users] Simulation in vaccum

[Mark Abraham]

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.

> and 
> 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...

Mark