[gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

[Nathan K Houtz]

Hello,

I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham:

Hi,
Try doing some EM and initial equilibration with no constraints at all, perhaps?
Mark

I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? 

Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start the simulation, which is incompatible with that command. Is there another way I can try to start the simulation unconstrained? Or would you suggest another idea to fix my shake warnings?

Thanks very much for your help,
Nathan

----- Original Message -----
From: "Nathan K Houtz" <nhoutz at purdue.edu>
To: gmx-users at gromacs.org
Sent: Monday, July 6, 2015 9:08:33 PM
Subject: trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

Hello,

I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that "shake failed to converge in 1000 steps" and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my simulation "blowing up." I tried decreasing the timestep down to 0.0001 ps, lowering the temperature, and minimizing further (down to 100 kJ/mol/nm) but nothing worked. I mostly used modified versions of the files available on this page: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_files_for_the_TIP4P/2005_model except the .gro file, which is my own. I did comment out the pressure coupling algorithms because I got a note that the barostat was unsuitable for equillibration, but I want NVT anyway. The temperature is 120.0 K and the coulomb type is PME. I've double checked and am satisfied with the interaction parameters in the topology file, so I'm out of ideas on where my mistake migh!
 t be. 

Here are the commands and files I used, in case it helps: 

> gmx grompp -f minim.mdp -c water_5100.gro -p water_topol.top -o em.tpr
> gmx mdrun -v -deffnm em
> gmx grompp -f water_5100.mdp -c em.gro -p water_topol.top -o water.tpr
> gmx mdrun -deffnm water

Here is the minim.mdp file:
http://textuploader.com/iggv

The water_topol.top file:
http://textuploader.com/igpd

And the water_5100.mdp file:
http://textuploader.com/igzj

You'll notice a slight mistake in the naming convention. There are 1700 molecules in the simulation, but everything is named something like '..._5100', even though tip4p water has a virtual site (making 4 particles). My .gro file does in fact have 6800 atoms, not 5100, I just neglected to rename the files because it's easier. Unfortunately I can't upload the .gro file because it's too big. I realize the problem could be there but I won't attach a large file unless it's specifically requested. Here's a sample:

Triclinic Frozen Water Simulation
 6800
    1WATER   OW    1   0.261   0.000   0.000  0.0000  0.0000  0.0000
    1WATER   HW    2   0.261   0.000   0.082  0.0000  0.0000  0.0000
    1WATER   HW    3   0.343  -0.000  -0.027  0.0000  0.0000  0.0000
    1WATER   DW    4   0.272   0.000   0.007  0.0000  0.0000  0.0000
    2WATER   OW    5   0.261   0.000   0.736  0.0000  0.0000  0.0000
    2WATER   HW    6   0.261   0.000   0.818  0.0000  0.0000  0.0000
    2WATER   HW    7   0.343   0.000   0.709  0.0000  0.0000  0.0000
    2WATER   DW    8   0.272   0.000   0.743  0.0000  0.0000  0.0000
    3WATER   OW    9   0.261   0.000   1.472  0.0000  0.0000  0.0000
    3WATER   HW   10   0.261   0.000   1.554  0.0000  0.0000  0.0000
    3WATER   HW   11   0.343   0.000   1.445  0.0000  0.0000  0.0000
    3WATER   DW   12   0.272   0.000   1.479  0.0000  0.0000  0.0000
    4WATER   OW   13   0.261   0.000   2.208  0.0000  0.0000  0.0000
    4WATER   HW   14   0.261   0.000   2.290  0.0000  0.0000  0.0000
    4WATER   HW   15   0.343   0.000   2.181  0.0000  0.0000  0.0000
    4WATER   DW   16   0.272   0.000   2.215  0.0000  0.0000  0.0000
    5WATER   OW   17   0.261   0.000   2.944  0.0000  0.0000  0.0000
    5WATER   HW   18   0.261   0.000   3.026  0.0000  0.0000  0.0000
    5WATER   HW   19   0.343   0.000   2.917  0.0000  0.0000  0.0000
    5WATER   DW   20   0.272   0.000   2.951  0.0000  0.0000  0.0000
    6WATER   OW   21  -0.130   0.677   0.000  0.0000  0.0000  0.0000
    6WATER   HW   22  -0.130   0.677   0.082  0.0000  0.0000  0.0000
    6WATER   HW   23  -0.048   0.677  -0.027  0.0000  0.0000  0.0000
    6WATER   DW   24  -0.119   0.677   0.007  0.0000  0.0000  0.0000
.
.
.
.
.
.
 1696WATER   OW 6781   1.825   3.160   0.276  0.0000  0.0000  0.0000
 1696WATER   HW 6782   1.784   3.232   0.304  0.0000  0.0000  0.0000
 1696WATER   HW 6783   1.907   3.161   0.304  0.0000  0.0000  0.0000
 1696WATER   DW 6784   1.830   3.170   0.283  0.0000  0.0000  0.0000
 1697WATER   OW 6785   1.825   3.160   1.012  0.0000  0.0000  0.0000
 1697WATER   HW 6786   1.784   3.232   1.040  0.0000  0.0000  0.0000
 1697WATER   HW 6787   1.907   3.161   1.040  0.0000  0.0000  0.0000
 1697WATER   DW 6788   1.830   3.170   1.019  0.0000  0.0000  0.0000
 1698WATER   OW 6789   1.825   3.160   1.748  0.0000  0.0000  0.0000
 1698WATER   HW 6790   1.784   3.232   1.776  0.0000  0.0000  0.0000
 1698WATER   HW 6791   1.907   3.161   1.776  0.0000  0.0000  0.0000
 1698WATER   DW 6792   1.830   3.170   1.755  0.0000  0.0000  0.0000
 1699WATER   OW 6793   1.825   3.160   2.484  0.0000  0.0000  0.0000
 1699WATER   HW 6794   1.784   3.232   2.512  0.0000  0.0000  0.0000
 1699WATER   HW 6795   1.907   3.161   2.512  0.0000  0.0000  0.0000
 1699WATER   DW 6796   1.830   3.170   2.491  0.0000  0.0000  0.0000
 1700WATER   OW 6797   1.825   3.160   3.220  0.0000  0.0000  0.0000
 1700WATER   HW 6798   1.784   3.232   3.248  0.0000  0.0000  0.0000
 1700WATER   HW 6799   1.907   3.161   3.248  0.0000  0.0000  0.0000
 1700WATER   DW 6800   1.830   3.170   3.227  0.0000  0.0000  0.0000
  4.07816  3.55416  3.75600  0.00000  0.00000 -1.77708  0.00000  0.00000  0.00000

Thanks very much for any help, I appreciate it. 
Nathan