Hi! I was trying to run a short md run on a domain of tubulin bound
with a ligand, using GB model to represent solvation effects. The part
till minimisation went fine, then I went on to equilibrate the
minimised structure using a file which contains the following lines,
# equilibrate structure #
&cntrl
imin=0
ntc=2, ntf=2,
cut=12.0, igb=1, saltcon=0.2, gbsa=1
ntpr=10,
nstlim = 5000, dt=0.002
ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
ntx=1,irest=0, ntb=0,
nscm = 1000,
ntr=1,
&end
The job is given as : sander -O -i equil.in -c 1sa0.rst -p
1sa0.top -ref 1sa0.rst -o 1sa0.equil.out -r 1sa0.equil.rst
However, the run is not completed and it ends abruptly without
generation the1sa0.equil.rst file , I have included the file which it
generates. Please could you help me out with this.
--
Devlina Chakravarty
JRF
Bose Institute
Kolkata
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Received on Thu May 12 2011 - 05:30:02 PDT
