Thanks a lot for your quick reply Justin. I got it. Turgay
2012/9/7 Justin Lemkul <jalem...@vt.edu>: > > > 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 -- 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