[gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)
Mark Abraham
mark.j.abraham at gmail.com
Tue Jul 7 09:17:11 CEST 2015
Hi,
Try doing some EM and initial equilibration with no constraints at all,
perhaps?
Mark
On Tue, Jul 7, 2015 at 3:09 AM Nathan K Houtz <nhoutz at purdue.edu> wrote:
> 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
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