[gmx-users] Non equilibrium MD

Satyan Sharma satti_dc at yahoo.com
Wed Jan 9 08:54:47 CET 2002

Hi all,
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
including the
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
like this

step 59
0, will finish at Sat Jan 12 12:46:51 2002Wrote pdb
files with previous
and current coordinates
Fatal error: 
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 
Many Thanks,

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