We wanted to use 2 slabs so that the net impuls is conserved. Also I'm looking at the slip length, so I actually want to extract the velocity profile of the water in between the two diamond slabs. I'm pulling in x (the pull setup is reproduced at the bottom of the old mail) and I'm using pbc in 3d.
What is the problem with pulling the diamond slabs at const speed? I don't actually care where exactly they are. I only care about the boundary condition at the diamond water interface (so that the diamond moves along the surface with v=cst). I mean, I'm pulling with "direction" not distance, why does "direction" care about the COM distance? Would it work with absolute coords (empty pullgroup0, pullgroup1=DIAM1 and pullgroup2=DIAM2)?? Alex Berk Hess schrieb: > Ah, maybe now I understand the issue. > Are you pulling in x and are the slabs periodic in x? > That will not work, as the COM is not defined in a periodic direction. > > If your slabs are very rigid, you might be lucky that it works > when you choose pull_pbcatoms for both groups that do not separate > more than half a box. > > But this experiment is much simpler with a single diamond slab > and the deform option to shear the box. > You can get the force from the off-diagonal pressure element. > > Berk > > >> Date: Wed, 2 Sep 2009 13:40:48 +0200 >> From: alexander.h...@mytum.de >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] t_trxframe speed units >> >> I'm studying shear flow, so I exspect the two slabs to be pulled in >> opposite x direction with the pull speed given. >> Looking at pull.xvg the slabs are pulled apart with about 1.5nm/ps until >> the box end (in x) is reached, then they jump back due to pbc. So this >> is what I would exspect, exept that the speed is much too high. >> >> hm..looking at the com speed vs time as per "g_traj -com -ov -n" for the >> first diamond slab only, >> the speed keeps increasing (see attached screenshot). Have I enabled a >> non constant pull rate somehow?? >> >> Alex >> >> Berk Hess schrieb: >> >>> Hi, >>> >>> Yes, speed is in nm/ps. >>> g_traj -com -ov -n will give the the speed of the slabs as a function >>> of time. >>> >>> If the speed is really 1.2 nm/ps, they should have moved 6 nm in 5 ns, >>> which is probably not the case, right? >>> >>> Could it be that you have pbc issues? >>> The distance between the two slabs could be taken within the box >>> or over the boundaries. >>> Have a look at pullx.xvg to see if it does what you expect. >>> (the time derivative of pullx.xvg should also give the speed >>> difference of the slabs). >>> >>> Berk >>> >>> >>>> Date: Wed, 2 Sep 2009 11:39:22 +0200 >>>> From: alexander.h...@mytum.de >>>> To: gmx-users@gromacs.org >>>> Subject: [gmx-users] t_trxframe speed units >>>> >>>> Hey, >>>> >>>> I averaged the speed of the diamond slabs, so I wrote a small gmx >>>> >>> tools which averages t_trxframe.v[i] where i iterates over the diam atoms. >>> >>>> I calc the avrg speed for a production run of 5ns after 0.5ns equilib >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.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 gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php