On 9/7/12 7:34 AM, Turgay Cakmak wrote:
Hi all,
I want to do Molecular dynamics simulation of a box of water (SPC
type). I get the spc216.pdb file from the gromacs/share/tutor.
Firstly, I did geometry optimization for nsteps= 50000.
Now, can I continue with production run or do I need to do
equilibration runs to arrive correct temperature and pressure?
Equilibration is always advisable, though for a system of water you don't do any
sort of position-restrained steps as you would if there were a solute. In any
case, if you do not run explicit NVT and/or NPT phases, you'll have to throw out
some of the beginning of the "production" trajectory anyway, since generation of
velocities does not guarantee that you maintain any sort of equilibrated state,
so the beginning of the run is equilibration. For stability reasons, NVT and
NPT are advisable. Water is pretty robust, but why take a chance when
equilibration steps are fast to do?
-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
