Hi all,
I tried to launch a MD with distance restraints (TAR: Time Average
Restriction). Consists of 8 staits, being the last of them this
restraint process.
The script is:
#!/bin/bash
################################
#SBATCH -t 10:00:00
#SBATCH -n 96
#SBATCH -p thinnodes
# SBATCH -p gpu-shared --gres=gpu # partitions with exclusive nodes
recomended for MPI jobs
#initialdir = /home/csic/car/mtr/myriam/smp-191ptn4syn
########################
module load intel/2016.4.258 impi/5.1.3.223
amber/16-at-17-patchlevel-10-15-cuda
####
srun pmemd.MPI -O -i ./tar/TAR.in -p ./leap/smp-191-ptn4rig.top -c
./pcte/smp-191-ptn4rig_pcon.rst -r ./tar/smp-191-ptn4rig_tar.rst -o
./tar/smp-191-ptn4rig_tar.out -inf ./tar/smp-191-ptn4rig_tar.info -e
./tar/smp-191-ptn4rig_tar.enr -x ./tar/smp-191-ptn4rig_tar.mdcrd -ref
./tar/smp-191-ptn4rig_pcon.rst
The TAR.in script is:
Restriction molecular dynamics
&cntrl
nmropt = 1, ntx = 5, irest = 1, ntpr = 1000, ioutfm = 0,
ntc = 2, ntf = 2, ntb = 2, pres0 = 1.0, taup = 2.0, ntp = 1,
cut = 8.0, imin = 0, nstlim = 8000000, dt = 0.001,
temp0 = 300.0, tempi = 300.0, ntt = 3, gamma_ln = 5.0,
ntwx = 1000, ntwr = 1000000, ig = -1,
/
&wt TYPE='REST', ISTEP1=0, ISTEP2=100000, VALUE1=0.0, VALUE2=1.0,
/
&wt TYPE='DISAVE', ISTEP1=0, ISTEP2=8000000, VALUE1=800.0, VALUE2=6.0,
/
&wt TYPE='DISAVI', ISTEP1=0, ISTEP2=1000, VALUE1=0.0, IINC=1,
/
&wt type='TORAVE', ISTEP1=0, ISTEP2=8000000, VALUE1=800.0, VALUE2=-1.0,
/
&wt type='TORAVI', ISTEP1=0, ISTEP2=1000, VALUE1=0.0, IINC=1,
/
&wt TYPE='END',
/
DISANG=./restraints.in
DUMPAVE=averst.out
LISTOUT=POUT
LISTIN=POUT
/
&end
And I have problems with my file restraints.in. When I carry out the
MD, it appears this error:
Warning: Error opening "Old" file from subroutine OPNMRG
File = ./restraints.in
The program can't open the file maybe for the route, or because the
nmropt is different to 0...I don't know
Any idea?
thank in advance
Myriam
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Received on Tue Sep 24 2019 - 02:00:03 PDT
