[gmx-users] Crash in water.

saurabh shakya shakya_79 at yahoo.com
Mon Dec 22 11:22:00 CET 2003

Hi all,
I am trying to run a md simulation of a protein in
which the cystines are attached to Fe. I have
calculated the charges on the cystines and iron ,using
nwchem ,and replaced the charges in the force field of
cystines with these. 
I ran a 1 ns md run of this system without water
..which went perfectly smooth. But when i tried the
same with water I always land up with Lincs warning in
one of the cystines .The max force after EM (without
water) is 56.908 while with water it is 3.22450e+06
which seems to be unusally high. I have tried both
flexspc and tip3pgmx water but it was of no help.
I would be grateful if anybody can suggest a reason
and a possible cure for this anomaly between
simulation with and without water.

With best regards

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