[gmx-users] Re: Re: Error- Simulation box resizes during mdrun

Justin Lemkul jalemkul at vt.edu
Fri Feb 8 17:29:44 CET 2013

On 2/8/13 2:51 AM, Bharath K. Srikanth wrote:
> Justin,
> You're right, the density of the box does increase during the simulation.

How large is the increase in density?

> But I don't believe the water is particularly sparse, since I've never
> encountered this issue in previous simulations, when I used these
> parameters for genbox while inserting water. The system density also
> appears to have an acceptable value in the beginning.
> Is there any other way I can approach this, for example, is there a
> command/md.mdp option that would fix the size of my simulation box to the
> initial values?

A fixed box is achieved by running in the NVT ensemble, but that may or may not 
be appropriate for membranes.


>> 3) I then re-inserted the peptide by editing the coordinate file, and ran
>> an energy minimization. Then I added water using genbox, and ran another
>> EM.
>> 4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was
>> happening, I observed that the size of the box was beginning to change, in
>> the z direction (not in the y direction as I said yesterday, but still,
>> parallel to the plane of the bilayer).
>> I've included some pictures here (in the .tga format), from before and
>> after the simulation. When I ran it in vmd using the initial coordinates
>> and the trajectory file, I could actually see the box resizing during the
>> run.
>> https://www.dropbox.com/l/UJuFbDTPaISIpkSf
>> I'm sure there's a very simple explanation, but I can't seem to figure it
>> out.
> It's hard to tell from the way things are rendered, but it seems to me
> that your
> water is very diffuse, and over the course of the simulation, the density
> of the
> system is increasing to try to fill a lot of void space.  A simple
> analysis of
> density should show this rather clearly.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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