[gmx-users] RE: Umbrella sampling question

Why not do two umbrella sampling simulations: one with initial conformations from your faster pulling and one with initial conformations from your slower pulling. Then you can run them both as regular US simulations until (a) neither US PMF is drifting systematically with increasing simulation

Re: [gmx-users] Re: Umbrella sampling question

Hi, Blindly defining the center of mass for a group of atoms is not possible in a periodic system such as a typical simulation box. You need some clue as to which periodic copy of every atom that is to be chosen. By providing pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the

Re: [gmx-users] Re: Umbrella sampling question

Thanks Erik! /PK 2012/11/16 Erik Marklund er...@xray.bmc.uu.se Hi, Blindly defining the center of mass for a group of atoms is not possible in a periodic system such as a typical simulation box. You need some clue as to which periodic copy of every atom that is to be chosen. By providing

Re: [gmx-users] Re: Umbrella sampling question

Hi Erik, Thank you for your answer. I see your point now. Went and had a look in gmx_wham.c to see how things are calculated, and that makes sense. I was looking for an easy way of relating different parts of the resulting PMF to my original starting frames, as a means to understand exactly

[gmx-users] Re: Umbrella sampling question

Hi Chris Seems my confusion was that I assumed that the distances in the profile.xvg-file should correspond to something I could measure with g_dist. Turns out it does not. Thank you for helping me sorting out this, I got it now :-) About pull_pbcatom0 though. My box is 2*1.08 nm in all

[gmx-users] Re: Umbrella sampling question

Hi Chris, and thank you for your reply. I should have included my g_dist command in my first mail. Here goes: I first run trjconv to extract the individual frames from my pulling trajectory $ trjconv -f pull.xtc -s pull.tpr -o conf.gro -sep -pbc mol -ur compact Then, g_dist like so: $ g_dist -s

[gmx-users] Re: Umbrella sampling question

What you reported is not what you did. It appears that grompp, gtraj, and g_dist report the same value. Please also report the value that you get from your pullx.xvg file that you get from mdrun, which I suspect will also be the same. The difference that you report is actually between the

Re: [gmx-users] Re: Umbrella sampling question

Hi, See below. 14 nov 2012 kl. 15.06 skrev Gmx QA: Hi Chris, and thank you for your reply. I should have included my g_dist command in my first mail. Here goes: I first run trjconv to extract the individual frames from my pulling trajectory $ trjconv -f pull.xtc -s pull.tpr -o