# Re: [AMBER] Trying to perform a heating MD in increments

From: Abelak, Kavin <kabelak.rvc.ac.uk>
Date: Tue, 4 Aug 2015 10:13:19 +0000

Dear Alaa,

I think you need to read through the manual (AMBER15, starting chapter 18.4) and look closely at what all the flags and parameters mean. I’m also fairly new to AMBER and the manual has proved very helpful.

I direct you to http://ambermd.org/tutorials/basic/tutorial3/section4.htm where a progressive heating script can be found. Although you have to be careful as this is for GB implicit solvent and you have to modify your parameters accordingly. To answer your specific question, it seems you need to put ntx=5 and irest=1.

As for “cut", I don’t think you’re meant to change it between sequential runs, but maybe someone with more experience can chip in here. And I think changing ntpr/ntwx will make analysing the results a bit tricky (also, writing every 5000 steps for a 25000 step run will only give you 6 data-points) unless you are analysing each heating segment individually.

Best of luck!

Regards,
Kavin

On 4 Aug 2015, at 09:39, Amber mail <amber.auc14.gmail.com<mailto:amber.auc14.gmail.com>> wrote:

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
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