Hi balaji,
I just got some results for my system with explicit water. Here is my input file:
&cntrl
imin = 0, ntx = 1, nstlim = 1000000,
dt = 0.001, ntc = 2, ntf = 2, tol = 0.000001,
tempi = 300.0, temp0 = 300.0,
scee = 1.2, cut = 9.0,
ntpr = 50, ntwx = 500, ntwr = 500,
ntt = 3, gamma_ln = 1.0,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
nscm = 0, nmropt = 1, ntr = 1,
restraint_wt=1.0,
restraintmask=':67-251,259-467.CA,C,N',
itgtmd = 1, tgtrmsd = 66.8998, tgtmdfrc = 0.1,
tgtrmsmask=":1-28",
/
&wt
TYPE='TGTRMSD', istep1=1, istep2=1000000,
value1 = 66.8998, value2 = 0.0,
/
&wt
type="END",
/
LISTOUT=POUT
DISANG=../../../14d.rst
I used a restraint file for my ligand, which may not needed for you.
I am doing test. Hope somebody having experience can give some comments.
All the best,
Shaowen
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of balaji nagarajan [balaji_sethu.hotmail.com]
Sent: Wednesday, April 15, 2009 10:19 AM
To: amber forumnew
Subject: [AMBER] help- regarding - TMD
Dear Amber ,
I am giving targeted molecular dynamics with explicit water
when i gave the following script
sander.MPI is running .
but when i see the out put file
tail -f tmdscript.out
its not printing any thing
I could not find our the error
help me out to solve this
the script as below
&cntrl
imin = 0,
irest = 0 ,
ntb = 2,
ntxo = 1,
ntx =1,
tempi =300.0,
ntc=2,
ntr =0,
ntf = 2,
nscm = 100,
ntwr = 100
ntpr = 100,
ntwx = 100,
ntwv =100,
ntwe = 100,
ntt = 3,
gamma_ln = 1.0,
temp0 = 300.0
nstlim = 2000000,
dt = 0.002,
cut = 10.0,
itgtmd=1,
tgtrmsd =0 ,
tgtmdfrc =0.01,
tgtfitmask= ":1- 76"
tgtrmsmask= ":1- 76"
/
regards
balaji
UOM
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Received on Wed May 20 2009 - 11:52:27 PDT
