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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
