You may try to add
tgtrmsd = xx.xxxx
/
&wt
TYPE='TGTRMSD', istep1=1, istep2=2000000,
value1 = xx.xxxxx, value2 = 0.0,
/
&wt
type="END",
/
to the end of your input file, where xx.xxxx is the rmsd of your initial "1-76" from the target.
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 Fri Apr 17 2009 - 01:09:30 PDT
