Hi yes, I tried pull_start=yes (you also suggested trying constraint instead of umbrella, which I tried as well). my box is rectangular.
Alex Berk Hess schrieb: > Hi, > > The only thing I suggested was using pull_start=yes, > otherwise you will start at a "random" distance and you will have enormous > forces. > Did you try that? > > Do you have a rectangular or a triclinic box? > > Berk > > >> Date: Thu, 3 Sep 2009 18:00:44 +0200 >> From: [email protected] >> To: [email protected] >> Subject: Re: [gmx-users] t_trxframe speed units >> >> Hey, >> >> I tried everything you suggested and a couple more things and still it >> is not possible to get a reasonable speed >> for the pulled groups (always way beyond the 0.01nm/ps set in the mdp >> file and mostly containing some high frequence patttern probably related >> to pbc). (I tried: constraint, pbcatoms, direction,position and using no >> ref group). >> >> Can I send you a small sample system with the problem or is there >> something else I can do? >> >> Thx, >> Alex >> >> Berk Hess schrieb: >> >>> But you can not talk about popping back, since there is pbc. >>> What matters is how the pull code determines the distance. >>> At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc, >>> such that it pulls smoothly even if the distance is larger than the box >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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
