My apologies for not providing the appropriate subject line before. You can delete the last post, to keep the archive more organized.<br><br><div class="gmail_quote">---------- <br><br>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.<br>
<br>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. <br><br>I added the flag -pforce 1000000 and I get the following output<br>
<br>....<br>199999992 steps, 100000.0 ps (continuing from step 100000000, 50000.0 ps).<br>step 100000000 atom 1444 x 13.886 25.151 4.660 force 1.00795e+06<br>step 100000000 atom 1687 x 9.419 20.258 13.016 force 1.00731e+06<br>
.....<br><br><br>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. <br>
<br>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<br><br>1444 13.886 8.231 4.660 <br>1687 9.419 3.338 13.016 <br><br>
and my pbc size is <br>16.92 16.92 16.92<br><br>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.<br><br>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.<br><br>thanks<br><br>-Paul<br><br><br><br>thanks<br><font color="#888888"><br>-Paul</font><div><div></div><div class="Wj3C7c"><br><br><br>
<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Message: 5<br>
Date: Thu, 11 Dec 2008 10:12:01 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] periodic boundary issue<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <BLU134-W4425B057F0648B0E8D6C8E8EF80@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Hi,<br>
<br>
I have not heard before about such problems.<br>
<br>
What did you do exactly?<br>
Did you continue your simulation the old fashioned way:<br>
tpbconv with a trajectory file?<br>
<br>
In 4.0 there are checkpoint files which can be read by mdrun -cpi,<br>
so you only need tpbconv to increase the number of steps in your tpr file.<br>
<br>
But the old fashioned way should still work.<br>
If there would be a pbc error I would expect the problems you describe<br>
to occur at step 0.<br>
<br>
Are you running in parallel?<br>
<br>
Berk<br>
<br>
Date: Wed, 10 Dec 2008 19:32:18 -0800<br>
From: <a href="mailto:pwhitfor@ctbp.ucsd.edu" target="_blank">pwhitfor@ctbp.ucsd.edu</a><br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] periodic boundary issue<br>
<br>
I am having the following issue with Gromacs 4.0.2:<br>
<br>
<br>
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<br>
<br>
<br>
<br>
<br>
Warning: 1-4 interaction between 1251 and 962 at distance 69.927 which is larger than the 1-4 table size 51.500 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
<br>
<br>
<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.0<br>
Source code file: nsgrid.c, line: 357<br>
<br>
<br>
<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each particle to a grid<br>
based on its coordinates. If your system contains collisions or parameter<br>
errors that give particles very high velocities you might end up with some<br>
<br>
<br>
<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where we detect those errors.<br>
Make sure your system is properly energy-minimized and that the potential<br>
<br>
<br>
<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -2147483648. It should have been within [ 0 .. 1331 ]<br>
<br>
-------------------------------------------------------<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
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.<br>
<br>
Thanks in advance<br>
<br>
-Paul<br>
<br>
<br>
<br>
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