15, 20, even 30 nm all result in the same effect, just at different rates. I didn't try anything larger than that - several of my systems would be dangerously close to being under 2x the cutoff radius across if I went even slightly higher.
--- Eric Jakobsson <[EMAIL PROTECTED]> wrote: > What is your van der Waals cut-off distance? From > our experience > years ago, we sometimes saw this if our van der > Waals cut-off was too > short; i.e., less than 15 angstroms. That seems > long, since it falls > off as sixth power, but because the long-range van > der Waals is all > attractive, there is no shielding (unlike the > electrostatic force). > > At 11:03 AM 4/6/2006, you wrote: > >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 > > --------------------------------- > Eric Jakobsson, Ph.D. > Professor, Department of Molecular and Integrative > Physiology, and of > Biochemistry, and of the Center for Biophysics and > Computational Biology > Senior Research Scientist, National Center for > Supercomputing Applications > Professor, Beckman Institute for Advanced Science > and Technology > 3261 Beckman Institute, mc251 > University of Illinois, Urbana, IL 61801 > ph. 217-244-2896 fax 217-244-2909 > > > > > _______________________________________________ > 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 > __________________________________________________ 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
