Ravi, not entirely sure what you are actually doing / aiming to do, but another option is to run the system NPT, which means the box size will scale to give the correct pressure / density, then you take that and run your NVT run. But that means you will end up with possibly a substantially smaller box, which may be an issue. But, closer you are to the correct starting point when you build the box the better.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Justin A. Lemkul > Sent: Thursday, 6 October 2011 9:35 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] NVT Equilibration > > > > Ravi Kumar Venkatraman wrote: > > *Dear All, > > But I scaled the solvent box according to the density > > using editconf_d command line. Then I carried out EM and NVT > equilibration.* > > > > Scaling the box with editconf simply scales the coordinates of the > molecules in > it, which may or may not produce a physically stable condition. > Building a > better starting box is the proper solution, as Dallas suggested. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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
