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
define=-DFLEXIBLE
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.
Chris.
######## 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.",
ir->init_t+step*ir->delta_t,owptr[error]+1);
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
2007-11-16
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