On 9/28/12 12:18 PM, pauladelgado wrote:
The distance restraint energy is arrond 13700 KJ/mol, is that ok?, but whta
happend with mi resulting pdb, i can't appreciate the distance restraint s i
made.
No, that's not OK. The very large value of energy suggests that the desired
distances are not being achieved (which you can measure with g_dist). How close
are the initial distances to the restraints you have set in the topology?
With respect to vacuum simulation, i am doing energy minimization and md
with no periodic boundaries, with coulombtype=Cutt-off and the cut-offs turn
off (equal to 0), and the md with no pressure and temperature cuopling, is
that ok? Also i am not going to do NVT and NPT because for what i understand
this is to equilibrate solvent and ions and make sure that this surround the
protein.
The purpose of any ensemble is to obtain a conformational ensemble under those
conditions. What it sounds like you're trying to do is run an NVE simulation,
which can be very difficult to obtain. See the notes on the wiki for
methodological issues.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
