Hello Experts,
I was running the REMD simulation. But due to some reasons it stopped.
Now I want to restart the simulation again. For restarting the
simulation I made the new input file same as the previous one, only
difference is that in place of ig = RANDOM_NUMBER I used ig = -1 for all
12 replicas in remd1.mdin file.
My remd1.mdin.001 file is given below:
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntt = 3,
gamma_ln = 2.0,
temp0 = 300.00,
ig = -1,
ntc = 2,
ntf = 2,
ntb = 0,
igb = 5,
cut = 999.0,
rgbmax = 999.0,
ntpr = 5000,
ntwx = 5000,
ntwr = 5000,
nmropt = 1,
nscm = 500,
numexchg = 10000,
nstlim = 25000,
dt = 0.002,
&end
/
&wt TYPE='END'
/
DISANG=/home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/1u
Then in remd1.groupfile I use -A flag in order to append output to
existing output files.
The command in groupfile for 12 replicas given below :
-A -rem 1 rem.log -i remd1.mdin.001 -o remd.mdout.001 -c remd.rst.001 -r
remd.rst.001 -x remd.mdcrd.001 -inf remd.mdinfo.001 -p 1urr.prmtop
Then I run this job with the command:
nohup mpirun -np 12 sander.MPI -ng 12 -groupfile remd1.groupfile &
But it is overwriting in output file, I am attaching the output file
named as remd.mdout.001.
When I use the same command with pmemd.cuda.MPI in place of sander.MPI
then it returns,
Running multipmemd version of pmemd Amber22
Total processors = 12
Number of groups = 12
unknown flag: -A
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf
mdinfo -l logfile]
[-ng numgroups -groupfile groupfile -rem remd_method]
[-rremd rremd_type -reservoir reservoir.nc]
[-hybridsolvent_remd_traj hybridsolvent_remd_traj_name]
[-amd amdlog_name -gamd gamdlog_name -scaledMD
scaledMDlog_name -suffix output_files_suffix]
[-sf sfout_name]
unknown flag: -A
unknown flag: -A
unknown flag: -A
unknown flag: -A
.............
Unknown flag for all 12 replica. I am not understanding why simulation
is not run with -A flag for appending the output and why simulation is
not running with pmemd.cuda.MPI and why it is overwriting the output
file as I use -A flag for append?
Thanking you
Munazzah Fatima Ansari
Ph.D Scholar
BARC-HBNI, Mumbai
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Received on Wed Apr 26 2023 - 06:30:02 PDT
