[gmx-users] Re: Water molecules cannot be settled, why?

[John Ladasky]

Date: Wed, 11 Jul 2012 10:32:35 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Re: Water molecules cannot be settled, why?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: 
<CABzE1Sj37c49x22yfPvFQniyQjfXjcgWw5dYcu0K9KZUcEiUww at mail.gmail.com>
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 > Hi John, Check where the unsettling water molecule is placed.
 > If it's in the protein. that may be the cause of the problem.
 > Otherwise, it's some of the other stuff you're doing, but rule
 > out the simple things first.
 > Cheers, Tsjerk

Thank you Tsjerk, I am proceeding with your recommendation.  I looked at 
two different simulations which crashed.  The unsettled water molecules 
appear to be far from the protein in all cases.

As the details of the protocol in the last message that I posted showed, 
I'm using five CPU cores for my simulations.  So the domain 
decomposition in mdrun is 5 x 1 x 1.  When the simulations crash, the 
error handling routine outputs only the domain which contains the 
unsettled water molecule.  In the first simulation that I examined, the 
domain was all solvent.  No protein atoms were present.

The crash occurred on step 81,240 of my final molecular dynamics run, 
and the atom that was identified as a problem was number 45191.  So I 
looked at the two PDB files that were dumped, and searched for atom 
45191.  I think that the first file describes the system immediately 
before the crash, and the second file shows the results of the bad 
calculations, am I correct?  Here is a selected portion of each file, 
showing atom 45191 and its neighbors:

step81240b_n4.pdb

ATOM  41009  OW  SOL     1      74.590  46.654  65.507
ATOM  41010  HW1 SOL     1      74.580  47.272  66.294
ATOM  41011  HW2 SOL     1      73.700  46.205  65.425
ATOM  43679  OW  SOL     1      71.579  49.011  70.894
ATOM  43680  HW1 SOL     1      71.730  49.197  69.924
ATOM  43681  HW2 SOL     1      71.013  49.735  71.288
ATOM  45191  OW  SOL     1      72.656  46.524  71.131
ATOM  45192  HW1 SOL     1      72.614  45.938  70.322
ATOM  45193  HW2 SOL     1      72.389  47.455  70.883
ATOM   6926  OW  SOL     1      75.926  46.701  73.317
ATOM   6927  HW1 SOL     1      75.024  46.674  72.886
ATOM   6928  HW2 SOL     1      76.564  47.194  72.724
ATOM  16016  OW  SOL     1      73.244  51.473  72.961
ATOM  16017  HW1 SOL     1      73.712  51.310  72.092
ATOM  16018  HW2 SOL     1      73.472  52.387  73.296

step81240c_n4.pdb

ATOM  41009  OW  SOL     1      74.582  46.669  65.502
ATOM  41010  HW1 SOL     1      74.582  47.320  66.260
ATOM  41011  HW2 SOL     1      73.689  46.221  65.445
ATOM  43679  OW  SOL     1    -66321836.00084864872.00046148104.000
ATOM  43680  HW1 SOL     1      71.706  49.216  69.937
ATOM  43681  HW2 SOL     1 1085546624.000-1490344960.000-271069120.000
ATOM  45191  OW  SOL     1    -176865.797532401.250-1222093.250
ATOM  45192  HW1 SOL     1    19264928.000-53927836.000125858544.000
ATOM  45193  HW2 SOL     1      72.351  47.488  70.877
ATOM   6926  OW  SOL     1      75.925  46.703  73.302
ATOM   6927  HW1 SOL     1      75.021  46.680  72.875
ATOM   6928  HW2 SOL     1      76.562  47.196  72.710
ATOM  16016  OW  SOL     1      73.240  51.478  72.957
ATOM  16017  HW1 SOL     1      73.728  51.296  72.103
ATOM  16018  HW2 SOL     1      73.442  52.407  73.266

WOW.  Something went seriously wrong with four atoms in that step. Are 
those even coordinates?  For some reason, atom 45191 was selected as the 
one to trigger the crash report.  I looked through the whole PDB file 
for other problems, and I found one more oxygen atom in another water 
molecule which had similarly wild coordinates.  It was half-way across 
the domain, not even a neighbor of atom 45191.

I had a look at atom 45191 in PyMol, and there was nothing obviously 
wrong with its position right before the crash. Stereo image here:

http://www.flickr.com/photos/15579975@N00/7553843726/

In the second crashed simulation, only a single abnormal atom was found 
in the PDB file.  The domain containing that water molecule did contain 
a part of the protein, but the water molecule was nowhere near the 
protein.  Here's an image of that domain (unsettled water molecule 
marked with an amber sphere):

http://www.flickr.com/photos/15579975@N00/7554770182/

I hope that helps to narrow down the problem.  Thanks again.