thanks for your help. My system ran fine for 250 ps but later the bilayer deformed very much. my mdp is integrator = md dt = 0.002 ; ps ! nsteps = 125000 ; total 100 ps. nstcomm = 1 nstxout = 250 nstenergy = 100 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = cut-off rcoulomb = 1.0 rvdw = 0.9 rlist = 0.9 ; Berendsen temperature coupling is on in two groups ; aniisotropic pressure coupling is now on Tcoupl = nose-hoover Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tc-grps = POPC SOL tau_t = 0.5 0.5 ref_t = 323 323 ref_p = 1 1 tau_p = 10 10 compressibility = 4.5e-5 4.5e-5 ; Energy monitoring energygrps = POPC SOL
Can anyone help? ---------------------------------------- > Date: Wed, 5 Dec 2007 11:27:40 +1100 > Subject: Re: [gmx-users] problem with npt > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > > > > > Dear users > > I was tyring to run an npt simulation of membrane. My mdp is: > > > As advised in a recent workshop on http://www.csc.fi/chem/course/gmx2007/ > > i am using Parrinello-Rahman instead of berendsen. The problem is that the > > box size is getting reduced to 9.99448 9.99448 9.25077 from 10.0 10.0 10.0 > > and water is compressing the bilayer. > > This is the purpose of equilibration with NPT - to fix density issues. The > contraction in Z suggests that your membrane is insufficiently dense in > that direction, or has some vacuum pockets. That's not a problem in itself > so long as you equilibrate long enough. Berendsen P-coupling will likely > do the same thing. > > > I also tried anisotropic coupling > > pcoupltype = anisotropic > > tc-grps = POPC SOL > > tau_t = 0.1 0.1 > > ref_t = 300 300 > > ref_p = 1 1 1 0 0 0 > > tau_p = 10 > > compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 > > This time my box size is reducing to 9.99065 9.99717 9.17646. > > I cant figure out the problem. Any help will be appreciated. > > This suggests the same non-problem exists. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _________________________________________________________________ Post free property ads on Yello Classifieds now! www.yello.in http://ss1.richmedia.in/recurl.asp?pid=221_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php