[gmx-users] How to delete bad water molecules

renying yren at home.ipe.ac.cn
Fri Nov 16 03:14:24 CET 2007

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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