Dear Justin, > Thanks for the reply.
The link you have mentioned says the parameters are for GROMACS 5.0 I am using an older version, 4.6.1 Is there another link/suggestions for that version. Thanks so much, Best, sxn > > > On 2/12/15 8:15 PM, shivangi nangia wrote: > >> Hello All, >> >> I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG >> using the script provided by Tsjerk) >> The system consists of popc, 21 AA protein, water and ions. >> >> After reverse CG I did short EM and 5 ns NVT simulation. >> However, when I do NPT simulation, the area per lipid drops from 67 ang2 >> to >> 57 within 1 ns ( x and y dimensions decrese and z increases). >> >> I am using semiisotropic pressure coupling. >> >> I have a question regarding that. >> I noticed in example .mdps and the tutorial by Justin Lemkul >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/membrane_protein/Files/npt.mdp >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/membrane_protein/Files/md.mdp >> >> >> tau_p is specified, the ref_p and compresibility is same, does not that >> mean essentially I am doing isotropic coupling? >> >> > No, that does not indicate isotropic pressure coupling. The full pressure > tensor is used to calculate pressures in the x-y and z dimensions > separately. The values of tau_p and compressibility are simply used for > calculating the response time of the barostat. > > The problem is that your nonbonded settings are incorrect: > > ; nblist cut-off >> rlist = 1.2 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> ; Method for doing electrostatics >> coulombtype = PME >> rcoulomb-switch = 0 >> rcoulomb = 1.2 >> fourierspacing = 0.16 >> pme_order = 4 >> optimize-fft = yes >> ; Method for doing Van der Waals >> vdw-type = switch >> ; cut-off lengths >> rvdw-switch = 1.0 >> rvdw = 1.2 >> >> > Note that potential switching leads to errors in the lipid force field. > You need a buffered neighbor list with force switching. The exact > parameters that you should use are listed on http://www.gromacs.org/ > Documentation/Terminology/Force_Fields/CHARMM. For lipids, you should > absolutely not deviate from these settings. The protein and nucleic acid > force fields (and the remainder of CHARMM additive models) should use these > settings, though they are more forgiving (i.e. potential switching does not > lead to noticeable artifacts). With lipids, the requirements are pretty > absolute. People frequently report a drop in APL; every time they do, it's > because they're using the wrong settings. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.