[gmx-users] periodic boundary issue

Berk Hess gmx3 at hotmail.com
Fri Dec 12 08:20:55 CET 2008


Could you mail me the new tpr file, checkpoint file
and the exact command line?


Date: Thu, 11 Dec 2008 17:26:20 -0800
From: pwhitfor at ctbp.ucsd.edu
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] periodic boundary issue

My apologies for not providing the appropriate subject line before.   You can delete the last post, to keep the archive more organized.


I am extending the run with tpbconv and a trajectory file.  I also get this error if I change the number of steps in the tpr by using tpbconv and then using a checkpoint to start the next run.  I get this error in both serial and parallel.

I used this same procedure for a system that did not cross a boundary and I had no problems.   I can provide you with the first tpr and the extended tpr if that would help.  

I added the flag -pforce 1000000 and I get the following output

199999992 steps, 100000.0 ps (continuing from step 100000000,  50000.0 ps).
step 100000000  atom   1444  x   13.886   25.151    4.660  force  1.00795e+06
step 100000000  atom   1687  x    9.419   20.258   13.016  force  1.00731e+06


This is on the first step of the simulation.   What is very odd is that these two atoms do not have a bond connecting them and they are not close to one another.   Since the forces are very close, gromacs  may be calculating an interaction between them.  

Here is another weird feature: if I look at the gro file that corresponds to the last frame of the previous run, these atoms coordinates are

1444  13.886   8.231   4.660 
1687   9.419   3.338  13.016 

and my pbc size is 
16.92 16.92 16.92

It appears that the y positions are being shifted out of the box, even though they are not close to the y boundaries.  Perhaps this is connected to the issue.

This system has ligands that are included as the same molecule substrate (in the
.top file they are all 1 big molecule), so perhaps gromacs thinks this is a periodic molecule because atoms are crossing different boundaries.  
About a year ago I had an issue with pdb=xyz versus full.  I had to use
full to get these systems to not explode when crossing a boundary.  My
understanding is that full is now been absorbed by xyz, so I should
just use xyz.  Also, there is no problem crossing boundaries during the
initial simulation.  It only has trouble on the first frame of the extended run.





Message: 5

Date: Thu, 11 Dec 2008 10:12:01 +0100

From: Berk Hess <gmx3 at hotmail.com>

Subject: RE: [gmx-users] periodic boundary issue

To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Message-ID: <BLU134-W4425B057F0648B0E8D6C8E8EF80 at phx.gbl>

Content-Type: text/plain; charset="iso-8859-1"


I have not heard before about such problems.

What did you do exactly?

Did you continue your simulation the old fashioned way:

tpbconv with a trajectory file?

In 4.0 there are checkpoint files which can be read by mdrun -cpi,

so you only need tpbconv to increase the number of steps in your tpr file.

But the old fashioned way should still work.

If there would be a pbc error I would expect the problems you describe

to occur at step 0.

Are you running in parallel?


Date: Wed, 10 Dec 2008 19:32:18 -0800

From: pwhitfor at ctbp.ucsd.edu

To: gmx-users at gromacs.org

Subject: [gmx-users] periodic boundary issue

I am having the following issue with Gromacs 4.0.2:

I run a simulation with pbc=xyz.   By the end of the simulation my molecule is split by the boundary (half of the molecule appears on one side and the other half on the opposite side).  This is not a problem.  The problem occurs when I use tpbconv to extend my run.  Then, within the first few steps (<100 steps) of the extended run I get messages like

Warning: 1-4 interaction between 1251 and 962 at distance 69.927 which is larger than the 1-4 table size 51.500 nm

These are ignored for the rest of the simulation

This usually means your system is exploding,

if not, you should increase table-extension in your mdp file

or with user tables increase the table size


Program mdrun, VERSION 4.0

Source code file: nsgrid.c, line: 357

Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or parameter

errors that give particles very high velocities you might end up with some

coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the potential

energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 1331 ]


What appears to be happening is that when the run is extended, the pbc is not imposed correctly, and the system explodes from all of the covalent bonds being stretched across the length of the box.  This also occurs if I take the final gro structure from the previous run and use grompp instead of tpbconv.  This occured in 20 different trajectories, all of which had run successfully with no issues for millions of time steps immediately before.

Any ideas what is going on?  I did not have this issue with the cvs version, but once 4.0 was released I started having this trouble.

Thanks in advance



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