If you want to use BD, the friction coefficient has to be large. Please check the manual. If you change your bd-fric to 5000, it might help.
On Wed, 2006-08-02 at 23:24 +0800, PAUL NEWMAN wrote: > Hi: > Thanks to everybody who helped me out with my last email. But now I > have another problem and I hope you can help me. As i told you I'm > doing a simulation of polyelectrolyte chain consisting of 50 charged > beads (-1) with 50 charged counterions(+1). My box simulation is 400 > nm x 400 nm x 400 nm and the polyelectrolyte length is 100 nm. My > problem is when I chage the intregator md to bd (position langevin > dynamics), it gives me Large VCM (group System) in the md.log file > and after some time it crashes at some point. When i take a look at > the energy file and plot the temperature I realized that the > temperature is far from the desired temperature. Please take a look at > my mdp file and help me figure out what i'm doing wrong. > My last question how can I choose the rlist, Vdw and coulomb cut-off > when I'm using PME and , for example my case in 400 nm x 400 nm x > 400 nm and 100 atoms with fourierspacing = 20 (is it ok?). Thanks in > advance. > ; By user: pcl > ; VARIOUS PREPROCESSING OPTIONS > title = Yo > cpp = /lib/cpp > include = > define = > > ; RUN CONTROL PARAMETERS > > integrator = bd > ; Start time and timestep in ps > tinit = 0 > dt = 0.0001 > nsteps = 100000000 > > comm-mode = Linear > > nstcomm = 1 > comm-grps = System > > ; LANGEVIN DYNAMICS OPTIONS > ; Friction coefficient (amu/ps) and random seed > bd-fric = 0.05 > ld_seed = 1993 > > > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 10 ; > ; ns algorithm (simple or grid) > ns_type = grid > ; Periodic boundary conditions: xyz (default), no (vacuum)or full (infinite > systems only) > > pbc = xyz > ; nblist cut-off > rlist = 100 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > ;rcoulomb-switch = 0 > > rcoulomb = 100 > fourierspacing = 20 > optimize_fft = yes > ; Relative dielectric constant for the medium and the reaction field > epsilon_r = 13.89354; > ; Method for doing Van der Waals > > vdw-type = Cut-off > rvdw-switch = 0 > rvdw = 100 > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = Berendsen > > ; Groups to couple separately > tc-grps = NA POL > ; Time constant (ps) and reference temperature (K) > tau_t = 0.01 0.01 > ref_t = 120.2717 120.2717; > > > ; Pressure coupling > Pcoupl = no > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = no > > ; OPTIONS FOR BONDS > constraints = none > > -- > Cheers, > > Paul > National Tsing Hua University (清A大W) > > xx你的兔 > I appreciate your help. Thanks! > Os agradezco la ayuda. Gracias! > > _______________________________________________ > gmx-users mailing list [email protected] > 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 _______________________________________________ gmx-users mailing list [email protected] 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
