Quoting s lal badshah <[EMAIL PROTECTED]>: > Dear Justin and Mark, > My pr.mdp file is: > > title = pr.mdp > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 > nsteps =100000 > nstcomm = 1 > nstxout = 250 > nstvout = 1000 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e5 > optimize_fft = yes > ;Berendsen temperature coupling is on > Tcoupl = berendsen > tau_t = 0.1 0.1 0.1 > tc-grps = protein SOL NA+ > ref_t = 298 298 298
Never couple solvent and ions separately. This has been discussed several times over the list. Read here for advice: http://wiki.gromacs.org/index.php/thermostats -Justin > ;Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ;Generate velocities is on at 298 K > gen_vel = yes > gen_temp = 298 > gen_seed = 173529 > > > As the warning is : > Step 1 Warning: pressure scaling more than 1%, mu: -2.6855e+10 -2.6855e+10 > -2.6855e+10 > > As the pressure is high so it shoud be how much? > Regards, > Lal badshah > > Send instant messages to your online friends http://uk.messenger.yahoo.com ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
