AMBER Archive (2009)

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

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (shaowen.hu-1_at_nasa.gov)
Date: Wed Apr 15 2009 - 12:56:07 CDT


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_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan [balaji_sethu_at_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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