I run md simulation of 10ns, and I want to restart another 10ns to
make 20ns using below file (prod.in) and commands. Please am I right
to proceed the process of restarting
10ns MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000
/
sander.MPI -O -i prod.in -o prod.out -p ds135.prmtop -c heat.rst -r
prod.rst -x prod.mdcrd -ref heat.rst
You can now use prod.rst file to produce another 10ns simulation by using,
sander.MPI -O -i prod.in -o prod1.out -p ds135.prmtop -c prod.rst -r prod1.rst -x prod1.mdcrd
and then you can further combine the two trajectories to get 20ns in one file. Plus ntr=0 in your input file, so you dont need to put -ref in the end.
Hope this helps,
SM
________________________________
From: Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>
Sent: Saturday, June 10, 2017 11:48:55 AM
To: AMBER Mailing List
Subject: [AMBER] How restart md simulation
Hello
I run md simulation of 10ns, and I want to restart another 10ns to
make 20ns using below file (prod.in) and commands. Please am I right
to proceed the process of restarting
10ns MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000
/
sander.MPI -O -i prod.in -o prod.out -p ds135.prmtop -c heat.rst -r
prod.rst -x prod.mdcrd -ref heat.rst
--
Warm regards
Mustafa Alhaji Isa
Bioinformatics and Computational BIology Lab,
Department of Biotechnology,
School of Engineering and Technology
Sharda University
Greater Noida, Delhi, India
Mob No.: +918800621829
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Received on Sat Jun 10 2017 - 04:30:02 PDT
