Hii all;
We are running equil step in amber GPU. the equil in file is looking like
this
"
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=1,
NTX=7,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
ntr=0,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=250000,
dt=0.002
/
" After finishing the job till step 13500 it shows an error " Nonbond cells
need to be recalculated, restart simulation from previous checkpoint with a
higher value for skinnb." As suggested previously not to worry about the
skinnb and restart it from previous good restart file (
http://archive.ambermd.org/201306/0376.html). Now I have the equil.rst file.
*Please let me know *
*1. How to restart now. I have the output files equil.out;equil.rst. How to
restart it from step 13500. I don't want to overwrite it. I want to write
the the remaining steps from 13500 till the last in the equil.out file
only.*
*Please let us know how to restart it now.*
Your help will be highly appreciated.
*Note: We use this command for submission of equil job " time mpirun -np 10
pmemd.cuda -O -i equil.in <
http://equil.in> -o equil.out -p
com_solvated.top -c Heating.rst -r equil.rst -x equil.mdcrd & "*
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Nov 07 2013 - 23:30:02 PST
