Hello all, I've been having some trouble recently with the leaflets in my bilayer gently drifting apart over a period of a few hundred picoseconds. Increasing the vdW radius hasn't helped (up to 2nm), although it did delay the seperation. Likewise, increasing tau_p from 5 up to 10. The really bizarre thing is that I've been simulating peptides in bilayers using 3.2.1 on our cluster for about 18 months now, using the lipid-modified version of ffgmx and the parameters listed below, and it's only since I've started using 3.3 on a new machine that I've had any trouble. Any suggestions on what might be going wrong?
title = Yo cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.0015 ; ps ! nsteps = 5000000 ; total 7500 ps. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid coulombtype = PME rlist = 1.5 rcoulomb = 1.5 rvdw = 1.5 pme_order = 8 fourierspacing = 0.2 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = DOPC SOL Protein Cl tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 ; Energy monitoring energygrps = DOPC SOL Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = surface-tension tau_p = 5 compressibility = 4.5e-5 4.5e-5 ref_p = 410 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
