[gmx-users] Non equilibrium MD
satti_dc at yahoo.com
Wed Jan 9 08:54:47 CET 2002
I am trying to simulate a ligand in enzyme active site
and for that I
have made a system in which all the atoms in shell
around the active site
are free to move. Then made another shell around it in
which the backbone
atoms are frozen and rest everything outside is frozen
water. The water molecules in both primary and
secondary shells are free
to move without any restraints. The energy
minimisation and PR were done
in routine way. But for full MD I am encountering a
fatal error which is
0, will finish at Sat Jan 12 12:46:51 2002Wrote pdb
files with previous
and current coordinates
t = 0.598 ps: Water molecule starting at atom 18819
can not be settled.
Check for bad contacts and/or reduce the timestep.
Could somebody help me with this.Just in case the few
parameters in mdp
file (for trail) are like this....
dt = 0.002
nsteps = 100000
freezegrps = FRZGRP
freezedim = Y Y Y
tc-grps = Couple FRZGRP
tau_t = 0.1 0.1
ref_t = 300 1
Pcoupl = no
constraints = all-bonds
I hav tried smaller time steps also. The group Couple
includes rest of the
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