Dear all,
I am a beginner user (dummy actually!!!) of AMBER, I create a input for minimization that runs on amber 14. Now I would like to use amber 16 (I would like to add Nosé Hoover thermostat in run production). I have the same topology file, the same initial coordinates and box size, the same input... and I launch sander. The simulation run, but sander, in AMBER 14 write output coordinates, instead in AMBER 16 does not write the output coordinates (this produces only a unreadable file of coordinates equal to that of restart).
I try with cpptraj but produce only atoms coordinates at the last step of simulation... I would like a trajectory
Could someone help me?
Thank you for your kind attention and for any hint.
Giovanna
in a bash script:
A=0
while [ $A -le 0 ]
do
P=$((A - 1))
echo RUNNING SANDER $A
srun --mpi=pmi2 sander.MPI -O -p ${TOP} -c Stac_md$P.rst -i Stac_md$A.in -o Stac_md$A.out -r Stac_md$A.rst -x Stac_md$A.crd -e Stac_md$A.en -v Stac_md$A.vel
echo SANDER $A STOPPED
cpptraj -p ${TOP} -y Stac_md$A.rst -x Stac_md$A.pdb
cpptraj -p ${TOP} -y Stac_md$A.rst -x prova.crd
A=$[$A+1]
done
Stac_md-1.rst is a initial amber coordinates file with box size
Input file is Stac_md0.in (Minimize and fix Ru atoms):
Minimize and fix Ru
&cntrl
ntb=0,
imin=1,
ntx=1,
irest=0,
maxcyc=30000,
ncyc=1000,
ntpr=1000,
ntwx=200,
cut=80.0,
nmropt=1,
ibelly=1,
bellymask='.2-85,87-142,144-199,201-256,258-297,299-338,340-379,381-420,422-461,463-502',
/
&wt type='REST', istep1=1, istep2=0, value1=10, value2=100/
&wt type='END' /
DISANG=rest0.RST
File rest0.RST arranges atoms at desired distance:
&rst restraint="distance(:1.N11,:4.Ru )", r1=1., r2=20, r3=20, r4=52.0,
rk2=0.268, rk3=0.268, r1a=1.000, r2a=20, r3a=20, r4a=52.0, rk2a=0.268, rk3a=0.268 /
&rst restraint="distance(:1.N24,:4.Ru )", r1=1., r2=20, r3=20, r4=52.0,
rk2=0.268, rk3=0.268, r1a=1.000, r2a=20, r3a=20, r4a=52.0, rk2a=0.268, rk3a=0.268 /
&rst restraint="distance(:1.N66,:3.Ru )", r1=1., r2=20, r3=20, r4=52.0,
rk2=0.268, rk3=0.268, r1a=1.000, r2a=20, r3a=20, r4a=52.0, rk2a=0.268, rk3a=0.268 /
&rst restraint="distance(:1.N51,:3.Ru )", r1=1., r2=20, r3=20, r4=52.0,
rk2=0.268, rk3=0.268, r1a=1.000, r2a=20, r3a=20, r4a=52.0, rk2a=0.268, rk3a=0.268 /
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Received on Wed Aug 08 2018 - 01:30:02 PDT
