[gmx-users] nstlist with vdw only
Would't this mean, that molecules could suddenly appear and lead to a discontinuity in the LJ-potential? Or in what way should I modify the r_vdw according to what rlist? I wanna end with a cut-off of the LJ-potentail around 1.75nm. Thanks in advance Nicolas Erik Lindahl wrote: Hi Nicholas, nstlist=1 means you recalculate the neighborlist every single step, which will be quite expensive. Depending on the type of system and temperature you are simulation you probably want to start somewhere around nstlist=10. Cheers, Erik On Aug 20, 2007, at 10:26 PM, Nicolas Schmidt wrote: Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/multimessengergmx_ethane_0365_32768.e74269ethane.itpethane_32768.topmd.mdp___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-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
Re: [gmx-users] nstlist with vdw only
Hi, On Aug 21, 2007, at 8:08 AM, Nicolas Schmidt wrote: Would't this mean, that molecules could suddenly appear and lead to a discontinuity in the LJ-potential? Or in what way should I modify the r_vdw according to what rlist? I wanna end with a cut-off of the LJ-potentail around 1.75nm. Certainly - but there will be a discountinuity even with nstlist=1 unless you use switch or shift modifications to the interaction. For perfect energy conservation you should pick rlist slightly larger than rvdw (depends on your charge group size and nstlist, but start with 0.2-0.3 nm), and apply switch or shift. However, there will be a bit of performance price to pay for that. Personally, I think energy conservation is overrated. There's nothing wrong with it, but energy conservation per se doesn't mean anything. You could use the potential V=sin(r) for Lennard-Jones interaction and still get conservation if it is switched smoothly to zero at the cutoff distance. The goal in most applications is to improve the accuracy of free energy, diffusion coefficients, or other observables, and then it is sometimes better to focus on the sampling and let thermostats take care of the drifts in energy. Cheers, Erik ___ gmx-users mailing listgmx-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
[gmx-users] nstlist with vdw only
Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/multimessenger gmx_ethane_0365_32768.e74269 Description: Binary data ethane.itp Description: Binary data ethane_32768.top Description: Binary data md.mdp Description: application/mdp ___ gmx-users mailing listgmx-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
Re: [gmx-users] nstlist with vdw only
Hi Nicholas, nstlist=1 means you recalculate the neighborlist every single step, which will be quite expensive. Depending on the type of system and temperature you are simulation you probably want to start somewhere around nstlist=10. Cheers, Erik On Aug 20, 2007, at 10:26 PM, Nicolas Schmidt wrote: Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/ multimessengergmx_ethane_0365_32768.e74269ethane.itpethane_32768. topmd.mdp___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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
