2009/9/22 <gmx-users-requ...@gromacs.org>
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > > > I will ty Justin's suggestion. I should have the answer by tomorrow. > > As for Thomas' suggestion, well, my mdp file didn't even have the > > "pull_start" flag. So I assume gromacs though I had set it to "no". But > > anyway, I checked the force in each window as you mentioned andfound > > something quite strange. The original pull_pf.xvg file, is an eve > > increasing line starting at -43 kj/mol/nm. So when I check a specific > > time frame, the pull force is, for example 93 kj/mol/nm at time frame > > 4000. But when I checked the pull force on the pull_pf.xvg file at that > > specific window, well, the pull force was something around -42 > > kj/mol/nm. Now I am really confused. It seems I am doing something > > really wrong, but actually quite simple to solve. I will try setting > > "pull_start = yes" and see what happens. > > Because you're looking at two entirely different things. In your initial > pulling simulation to separate your species, the force will continually > change, > building up until the two dissociate, then probably level off to some > roughly > constant value until the simulation stops (when the species are no longer > interacting). > > In umbrella sampling, the force imposed on the pull group is used to > restrain it > within a window, and will not necessarily have anything to do with the > values > obtained in the original separation simulation. Apples to oranges, if you > will. > > Setting "pull_start = yes" is appropriate for the umbrella sampling. In > conjunction with "pull_init1 = 0" the original distance between the two > species > should be taken as the distance to be restrained during umbrella sampling > simulations. > > > One other thing. I checked my pull_px.xvg file for the initial > > separation trajectory. It looks like a a rollercoaster with a tendency > > to going down. So the final value of distance PULL_COM is 1.5nm lower > > than the initial value. The values on each of my windows are the same > > for the individual values pf the separation trajectory from which they > > were taken. And again, the values on the pull_px,xvg files all decrease. > > > > Not a steady increase as the two species separate? Is your box size > sufficient > to accommodate the distance you are pulling, or are you experiencing > periodicity > artefacts? > > > I am sorry. Correcting. The px values increase for my simulation. The files I checked were for a simulation with a smaller box periodicity does occur. With my actual system (larger box) the px values increase. I have started a new run for my windows setting "pull_start = yes" with "pull_init1 = 0". Once I have some of the simulations finished I should have an idea of what is happening. Thank you
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