[gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water
gmx3 at hotmail.com
Tue Mar 30 16:01:20 CEST 2010
> Date: Tue, 30 Mar 2010 08:13:11 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water
> Ozge Engin wrote:
> > Hi all,
> > First of all, thank you for your quick reply Justin. Here, I want to
> > state the problem in a clearer way.
> > I have been trying to calculate the PMF between two NA+ ions in explicit
> > water. In order to do that I first pulled one of the NA+ ions
> > continuously with respect to the other until the farthest point on the
> > PMF curve was reached. After that I split the continuous pulling
> > trajectory from the points that are in correspondence with the
> > constraint points of the PMF curve. These were done via *genera_start_4*
> > script.
> You don't have a PMF curve. I expect you're referring either to the pullf.xvg
> or pullx.xvg files generated from the COM pulling output. PMF is calculated
> later, through umbrella sampling.
> > I took each starting conformation, that was obtained from continuous
> > pulling, solvated with water, and then energy minimized. Then, I
> > prepared the systems for constraint pulling MD production runs. These
> Weren't these systems already solvated in the above pulling? If you add water
> differently to each system, you may get unreliable results. Use
> water-containing configurations from the original SMD trajectory (above) as your
> input configurations.
> > were done via *input* script. Interestingly, systems (ion+water) at some
> > of the constraint points could not been energy minimized, it reached to
> > the machine epsilon, but not to the desired criteria. The force per atom
> > was too high, around the order of ^4. Moreover, this issue was not
> > distance-dependent, which means that the energy minimization worked for
> > smaller constraint points, but not for some of the larger constraint
> > points. When I looked at the problematic trajectories, I saw that bonds
> > of a water molecule near the box boundary was longer. I thought that
> > this may be due to genbox command. Because of the small radius of NA+
> Perhaps. See the above comment. It's better to not re-solvate after the fact.
> Was the initial pull actually conducted in vacuo?
> > ion it may not check the overlaps among the atoms. In order to test
> > whether it is the case I increased the LJ parameters of the ion. This
> > worked for some of the points, but not for others. (Note that the
> > diameter is still smaller than the constraint distance between the two
> > ions.)
> > I use ffG45a3 force field, and the scripts given above. I tried this
> > with different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar
> > problems.
> Is the total pull distance less than half the box vector along which you are
> pulling? If not, you will be getting bizarre behavior from the pull code
> related to PBC.
> Also realize that when you say you are doing constraint pulling, it will require
> some trickery to calculate the PMF after your simulations are done. What you
> want is umbrella sampling. You can get the PMF from constraint forces, but
> there is no automated tool to do this in Gromacs (see the list archive for a few
> posts on how you could approach that). I'd say make your life easy and use
> umbrella sampling for the actual data collection :)
I don't agree with that.
Constraining is simpler, since you can simply integrate the mean force
(you have to take care with the entropy effect, but that old holds for
Anyhow, I assume Ozge is using a script I provided her.
I can clean that up and post it if it is of general use.
> > Kind Regards
> > --
> > Ozge Engin
> > ★☆
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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