Dear AMBER users,
I performed a minimization for a protein, and I want to perform 50ps of
heating MD at 100K. Then I will heat up the system in increments of 25K
with 50ps of MD simulation at each temperature increment until the desired
temperature of 310K is established.
I just want to make sure that I am on the right track!
What I have done to perform this run is that I created the heat input files
as follows
heat100.in
Heat100K
&cntrl
imin=0,
ntx=1,
irest=0,
nstlim=25000,
dt=0.002,
ntf=2,
ntc=2,
tempi=0.0,
temp0=100.0,
ntpr=100,
ntwx=100,
cut=8.0,
ntb=2,
ntp=1,
ntt=3,
gamma_ln=1.0,
tautp=1.0,
taup=1.0,
pres0=1.01325,
nmropt=0
/
heat125.in
Heat125K
&cntrl
imin=0,
ntx=1,
irest=0,
nstlim=25000,
dt=0.002,
ntf=1,
ntc=2,
tempi=100.0,
temp0=125.0,
ntpr=5000,
ntwx=5000,
cut=10.0,
ntb=2,
ntp=1,
ntt=3,
gamma_ln=1.0,
tautp=1.0,
taup=1.0,
pres0=1.01325,
nmropt=0,
/
The running commands from the script are
mpirun -np 40 ${DIR_NAME} -O -i heat100.in -o ${FILENAME}_100K.out -p
${TOPNAME}.top -c ${FILENAME}_min.res -r ${FILENAME}_100K.res -x
${FILENAME}_100K.crd -ref ${FILENAME}_min.res
mpirun -np 40 ${DIR_NAME} -O -i heat125.in -o ${FILENAME}_125K.out -p
${TOPNAME}.top -c ${FILENAME}_100K.res -r ${FILENAME}_125K.res -x
${FILENAME}_125K.crd -ref ${FILENAME}_100K.res
mpirun -np 40 ${DIR_NAME} -O -i heat150.in -o ${FILENAME}_150K.out -p
${TOPNAME}.top -c ${FILENAME}_125K.res -r ${FILENAME}_150K.res -x
${FILENAME}_150K.crd -ref ${FILENAME}_125K.res
mpirun -np 40 ${DIR_NAME} -O -i heat175.in -o ${FILENAME}_175K.out -p
${TOPNAME}.top -c ${FILENAME}_150K.res -r ${FILENAME}_175K.res -x
${FILENAME}_175K.crd -ref ${FILENAME}_150K.res
mpirun -np 40 ${DIR_NAME} -O -i heat200.in -o ${FILENAME}_200K.out -p
${TOPNAME}.top -c ${FILENAME}_175K.res -r ${FILENAME}_200K.res -x
${FILENAME}_200K.crd -ref ${FILENAME}_175K.res
mpirun -np 40 ${DIR_NAME} -O -i heat225.in -o ${FILENAME}_225K.out -p
${TOPNAME}.top -c ${FILENAME}_200K.res -r ${FILENAME}_225K.res -x
${FILENAME}_225K.crd -ref ${FILENAME}_200K.res
mpirun -np 40 ${DIR_NAME} -O -i heat250.in -o ${FILENAME}_250K.out -p
${TOPNAME}.top -c ${FILENAME}_225K.res -r ${FILENAME}_250K.res -x
${FILENAME}_250K.crd -ref ${FILENAME}_225K.res
mpirun -np 40 ${DIR_NAME} -O -i heat275.in -o ${FILENAME}_275K.out -p
${TOPNAME}.top -c ${FILENAME}_250K.res -r ${FILENAME}_275K.res -x
${FILENAME}_275K.crd -ref ${FILENAME}_250K.res
Am I doing right? I am not sure If I have to put ntx=5, irest=1 in my
heat input files in order to make my heating MD simulation sequential? What
I am thinking of is that the commands above already will be performed in
sequential manner since the files flaged with -c will get every coordinate
file from the previous run.
I appreciate If you could help me
Thanks in advance!
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Received on Tue Aug 04 2015 - 02:00:02 PDT
