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<br><br>> Date: Tue, 30 Mar 2010 08:13:11 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] problem with the energy minimization of a system        composed of two NA+ ions and explicit water<br>> <br>> <br>> <br>> Ozge Engin wrote:<br>> > Hi all,<br>> > <br>> > First of all, thank you for your quick reply Justin. Here, I want to <br>> > state the problem in a clearer way.<br>> > <br>> > I have been trying to calculate the PMF between two NA+ ions in explicit <br>> > water. In order to do that I first pulled one of the NA+ ions <br>> > continuously with respect to the other until the farthest point on the <br>> > PMF curve was reached. After that I split the continuous pulling <br>> > trajectory from the points that are in correspondence with the <br>> > constraint points of the PMF curve. These were done via *genera_start_4* <br>> > script.<br>
> > <br>> <br>> You don't have a PMF curve. I expect you're referring either to the pullf.xvg <br>> or pullx.xvg files generated from the COM pulling output. PMF is calculated <br>> later, through umbrella sampling.<br>> <br>> > I took each starting conformation, that was obtained from continuous <br>> > pulling, solvated with water, and then energy minimized. Then, I <br>> > prepared the systems for constraint pulling MD production runs. These <br>> <br>> Weren't these systems already solvated in the above pulling? If you add water <br>> differently to each system, you may get unreliable results. Use <br>> water-containing configurations from the original SMD trajectory (above) as your <br>> input configurations.<br>> <br>> > were done via *input* script. Interestingly, systems (ion+water) at some <br>> > of the constraint points could not been energy minimized, it reached to <br>> > the machine
epsilon, but not to the desired criteria. The force per atom <br>> > was too high, around the order of ^4. Moreover, this issue was not <br>> > distance-dependent, which means that the energy minimization worked for <br>> > smaller constraint points, but not for some of the larger constraint <br>> > points. When I looked at the problematic trajectories, I saw that bonds <br>> > of a water molecule near the box boundary was longer. I thought that <br>> > this may be due to genbox command. Because of the small radius of NA+ <br>> <br>> Perhaps. See the above comment. It's better to not re-solvate after the fact. <br>> Was the initial pull actually conducted in vacuo?<br>> <br>> > ion it may not check the overlaps among the atoms. In order to test <br>> > whether it is the case I increased the LJ parameters of the ion. This <br>> > worked for some of the points, but not for others. (Note that the <br>> >
; diameter is still smaller than the constraint distance between the two <br>> > ions.) <br>> > <br>> > I use ffG45a3 force field, and the scripts given above. I tried this <br>> > with different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar <br>> > problems.<br>> > <br>> <br>> Is the total pull distance less than half the box vector along which you are <br>> pulling? If not, you will be getting bizarre behavior from the pull code <br>> related to PBC.<br>> <br>> Also realize that when you say you are doing constraint pulling, it will require <br>> some trickery to calculate the PMF after your simulations are done. What you <br>> want is umbrella sampling. You can get the PMF from constraint forces, but <br>> there is no automated tool to do this in Gromacs (see the list archive for a few <br>> posts on how you could approach that). I'd say make your life easy and use <br>> umbrella sampling
for the actual data collection :)<br><br>I don't agree with that.<br>Constraining is simpler, since you can simply integrate the mean for
ce<br>(you have to take care with the entropy effect, but that old holds for<br>umbrella sampling).<br>Anyhow, I assume Ozge is using a script I provided her.<br>I can clean that up and post it if it is of general use.<br><br>Berk<br><br>> <br>> -Justin<br>> <br>> > Kind Regards<br>> > <br>> > -- <br>> > Ozge Engin<br>> > ★☆<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at htt
p://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>                                            <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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