[gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water

Berk Hess 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
umbrella sampling).
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.


> -Justin
> > Kind Regards
> > 
> > -- 
> > Ozge Engin
> > ★☆
> > 
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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