<br><br><div class="gmail_quote">2009/9/22 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
<br>
> I will ty Justin's suggestion. I should have the answer by tomorrow.<br>
> As for Thomas' suggestion, well, my mdp file didn't even have the<br>
> "pull_start" flag. So I assume gromacs though I had set it to "no". But<br>
> anyway, I checked the force in each window as you mentioned andfound<br>
> something quite strange. The original pull_pf.xvg file, is an eve<br>
> increasing line starting at -43 kj/mol/nm. So when I check a specific<br>
> time frame, the pull force is, for example 93 kj/mol/nm at time frame<br>
> 4000. But when I checked the pull force on the pull_pf.xvg file at that<br>
> specific window, well, the pull force was something around -42<br>
> kj/mol/nm. Now I am really confused. It seems I am doing something<br>
> really wrong, but actually quite simple to solve. I will try setting<br>
> "pull_start = yes" and see what happens.<br>
<br>
Because you're looking at two entirely different things. In your initial<br>
pulling simulation to separate your species, the force will continually change,<br>
building up until the two dissociate, then probably level off to some roughly<br>
constant value until the simulation stops (when the species are no longer<br>
interacting).<br>
<br>
In umbrella sampling, the force imposed on the pull group is used to restrain it<br>
within a window, and will not necessarily have anything to do with the values<br>
obtained in the original separation simulation. Apples to oranges, if you will.<br>
<br>
Setting "pull_start = yes" is appropriate for the umbrella sampling. In<br>
conjunction with "pull_init1 = 0" the original distance between the two species<br>
should be taken as the distance to be restrained during umbrella sampling<br>
simulations.<br>
<br>
> One other thing. I checked my pull_px.xvg file for the initial<br>
> separation trajectory. It looks like a a rollercoaster with a tendency<br>
> to going down. So the final value of distance PULL_COM is 1.5nm lower<br>
> than the initial value. The values on each of my windows are the same<br>
> for the individual values pf the separation trajectory from which they<br>
> were taken. And again, the values on the pull_px,xvg files all decrease.<br>
><br>
<br>
Not a steady increase as the two species separate? Is your box size sufficient<br>
to accommodate the distance you are pulling, or are you experiencing periodicity<br>
artefacts?<br>
<br>
<br></blockquote><div>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.<br>
Thank you<br></div></div><br>