[gmx-users] Strange pressure coupling behaviour, rapid expanding box

Justin Lemkul jalemkul at vt.edu
Thu Dec 22 13:54:27 CET 2016

On 12/21/16 3:25 PM, Kamps, M. wrote:
> Dear GMX users,
> I'm experiencing difficulties with my simulation.
> I have created a ionic bonded, rough surface of gold atoms (3276
> atoms) in the OPLS FF, which is held together with Lennard-Jones
> interactions. In the same box I've placed a C4H10 (14 atoms) molecule,
> although the problem also occurs with proteins. This box is then
> solved using SPCE water, although I've also tried TIP4P water.
> The box size is originally 5.4x5.4x4.5 nm, and is first energy
> minimized and NVT equilibrated. Up to this point the system behaves
> normal and I can't see any red flags. When I then want to NPT
> equilibrate the system, something strange happens. The periodic box
> seems to ´explode´, since it rapidly (but constantly) expands. The
> final dimensions are 5.4x5.4x24 nm after 50ps.
> Analyzing the outputs of the NPT equilibrium shows some strange
> things: The initial pressure starts at roughly 14000 bar and rapidly
> decreases to around 3000 bar at t=5ps, after which it linearly
> decreases to 2000 bar. Since the box is rapidly expanding, the volume
> of the system is linearly growing, starting at roughly 160nm3 and
> expanding to 850nm3 at 50ps.
> I've added two screenshots, one before and one after the simulation.
> I've also uploaded a screenshot of my mdp file, since it is easier to
> read from an image than in here (i think).
> https://s23.postimg.org/yceosj0q3/Before.png
> https://s23.postimg.org/9kjceaobv/After.png
> https://s24.postimg.org/xrzza3mt1/NPT_mdp.png
> My system uses a semiisotrpic pcoupletype, since I want different
> behaviour in xy and z direction. The reference pressure has been set
> to 1 atmosphere (almost 1 bar), while the compressibility in the xy
> direction is that of the material, while in the z direction it is that
> of water. I only want periodic boundary conditions in the xy
> directions, and both the z planes are LJ 12-6 walls. At z=0 the wall
> is behaving like the same gold atoms, with the corresponding LJ
> potential, while the upper wall is exerting an LJ potential of a dummy
> atom (so no LJ interaction). Might this cause the error? I varied a

Probably.  A dummy wall is no wall at all.  MNH3 has zero for its sigma and 
epsilon, so it won't have any interaction with anything.


> lot with the wall-r-linpot option, but putting in an positive,
> negative or zero value does not seem to make a difference.
> Are there any ideas as to what I am doing wrong? Thanks in advance,
> Mark


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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