Dear Amber users
Iam trying to run explicit solvent CpHMD calculations as outlined in
tutorial: http://jswails.wikidot.com/explicit-solvent-constant-ph-md
I managed to get all the output files for the minimization and heating
steps, I tried to run the equilibration step but I cannot get the
*-cprestrt* *.cpin* file form the equilibration step. What could be the
problem?
The calculation only produced the following files: .mdout, cpout,.nc and
rst7
I used the following commands:
mpirun -np 24 -machinefile $PBS_NODEFILE $exe -O -i md.mdin -p
3LZT.solv10.parm7 -c 3LZT.solv10.heat.rst7 -cpin 3LZT.solv10.cpin -o
3LZT.solv10.equil.mdout -cpout 3LZT.solv10.equil.cpout -r
3LZT.solv10.equil.rst7 -cprestrt 3LZT.solv10.equil.cpin -x
3LZT.solv10.equil.nc
md.in script:
Explicit solvent molecular dynamics constant pressure MD
&cntrl
imin=0, irest=1, ntx=5,
ntpr=1000, ntwx=1000, nstlim=2000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=1.0, ig=-1,
ntp=1, ntc=2, ntf=2, cut=8,
ntb=2, iwrap=1, ioutfm=1,
/
Thank you
Tebello
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 10 2017 - 07:00:02 PST
