AMBER Archive (2009)

Subject: RE: [AMBER] help- regarding - TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Thu Apr 16 2009 - 12:01:39 CDT

DEAR AMBER !

I am doing Targeted molecular dynamics for DNA structure which are different but from the same sequence

i have already posted my problem and got
many sugesstions
I can able to run this in vaccum ,
but i can not do this in explicit water with periodic condition
if i give ntb = 2
its not writting the out put files
but the sander.MPI is running in the job if i give top

i have given my input script 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"
> > /

could any one suggest me how to fix it

thank you in advance
balaji
UOM

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