[gmx-users] How to delete bad water molecules

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Nov 16 05:53:36 CET 2007

I don't know the answer to the exact question that you have posed, but  
I instead suggest that getting rid of that water molecule is not a  
good idea. You should rather minimize your system. While minimizing,  
be sure to include


in your .mdp file

Try running 500 steps of steep and then 500 steps of l-bfgs, that is  
usually enough for me. Also, be sure to run grompp_d and mdrun_d for  
double precision in the EM portion even if you will use single  
precision for the MD section.

Then remember to NOT include the define=-DFLEXIBLE for the subsequent md run.


########  Original Message ###########

I'm  dealing with a large system of proteins in water molecules of SPC  
model on GMX 3.3.1. When doing position restraints, it always gives  
such error info as follows and then stops:
t = 0.002 ps: Water molecule starting at atom 72750 can not be settled.
Check for bad contacts and/or reduce the timestep.

This error comes from src/mdlib/constr.c:
       if (!bOK && bDumpOnError==1)
	fprintf(stdlog,"\nt = %.3f ps: Water molecule starting at atom %d can  
not be "
		"settled.\nCheck for bad contacts and/or reduce the timestep.",

I want to check this naughty guy out and test whether gmx can run  
without this bad water molecule.The question is, there are ~500,000  
atoms in the system and the figure  72750 shows up 5 times. How can I  
know which one is the bad water molecule? Is it the ?72750th  
(?=0,1,2,3,4) atom in the whole system or just in water molecules?

//description of proteins
ATOM      1  N   ALA     1      65.430  66.090  97.040  1.00  0.00
//description of water
ATOM  73347  OW  SOL  8016       5.700  12.790  11.830  1.00  0.00
ATOM  73348  HW1 SOL  8016       4.860  12.540  11.310  1.00  0.00
ATOM  73349  HW2 SOL  8016       5.770  13.800  11.860  1.00  0.00

Any help would be appreciable.Thank you all in adcance.

Ying  Ren

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