I will try this, thx for the help. Anyways, what is the correct way to do what I want with gromacs 4? (apparently the setup I tryed to use worked for gromacs 3, since I ported the input data from old sims and now I'm trying to recreate the old results).
Alex Berk Hess schrieb: > The simple issue is that a center of mass is not uniquely defined > for a periodic group of particles. > If you work on the velocity level, this problem is easy to solve. > But the pull code works on the coordinate level. > > Try with pull_pbcatom set, it might work. > > Berk > > >> Date: Wed, 2 Sep 2009 14:11:11 +0200 >> From: [email protected] >> To: [email protected] >> Subject: Re: [gmx-users] t_trxframe speed units >> >> 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 >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
