Hi Hirdesh,
Why don't you consider changing temp0 = 100.0 for first 10ps
and then switch to ntb=2 (constant pressure) and increase your
temp0 to 300 for another 20 ps.
I had problem in equilibrating the solvent around protein-ligand complex and
the following runs fixed the problem (Thanks to Dr. Ross Walker)
you can try the following template for parameters.
run # 1
&cntrl
imin = 0,
ntpr = 100,ntwx = 100, ntwr = 1000,
nstlim = 10000,dt = 0.001,
tempi = 0.0, temp0 = 100.0,
ntb = 1,
ntr = 1,
cut = 8.0,
ntt = 3, gamma_ln = 1.0
/
Hold the protein fixed
10.0
RES 1 122
END
END
run # 2
&cntrl
imin = 0,irest=1, ntx=7,
ntb=2, pres0=1.0, ntp=1,
taup=2.0,
ntpr = 100,ntwx = 100, ntwr = 1000,
nstlim = 20000,dt = 0.001,
tempi =100.0, temp0 = 300.0,
ntr = 1,
cut = 8.0,
ntt = 3, gamma_ln = 1.0
/
Hold the protein fixed
10.0
RES 1 122
END
END
Good luck,
Senthil
________________________________
From: hirdesh kumar <hirdeshs8.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, September 3, 2010 4:51:49 AM
Subject: [AMBER] Heating up the sytem
Hi All,
I want to heat my system slowly to prevent artifacts generation. I run the
below mentioned script for initial heating equilibration. But still the
system got heated up very quickly and within 3ps interval the temprature
reaches to 276 K. i need help regarding heating the system slowly.
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nrespa=2,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000,
/
Keep Protein fixed with weak restraints
10.0
RES 1 122
END
END
--
Hirdesh
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Received on Sat Sep 04 2010 - 08:00:04 PDT
