You need to look through the tutorials. Minimization is not done for a
length of time, but for a number of steps. You then "equilibrate" for a
length of time before production dynamics. Here are some examples of my
minimization and equilibration scripts:
Initial minimization
&cntrl
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 0, ntwv = 0, ntwe = 0,
ntf = 1, ntb = 0,
ntc = 1, igb = 6,
cut = 40.0,
imin = 1,
maxcyc = 1000,
ncyc = 100,
&end
Simple MD in vacuum
&cntrl
imin=0, irest=0, ntx=1,
nstlim=125000, dt=0.001,
ntc=2, ntf=2,
ntt=1, tautp=0.5,
tempi=300.0, temp0=300.0,
ntpr=10000, ntwx=50000, ntwr=250000,
ntb=0, igb=6,
cut=9999.,rgbmax=9999.
restraintmask=':1-9999',
restraint_wt=0.5,
&end
For each input deck, it's pmemd -O -i mdin (name of deck) -c (name of input
coords) -p (name of topology) -o (name of output) -x (trajectory) -r
(restart)
Your inputs will differ based on your needs and the system you are studying.
Dave
On Tue, Jun 11, 2019 at 2:11 PM Charu Sharma (JRF) <
charu.sharma.lnmiit.ac.in> wrote:
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> From: "Charu Sharma (JRF)" <charu.sharma.lnmiit.ac.in>
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> Date: Tue, 11 Jun 2019 23:35:16 +0530
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> * Dear all ,*
>
> *I want to know how to do minimization of 100 ps and production run for 500
> ps* * for explicit solvent .*
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