AMBER Archive (2009)

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

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Thu Apr 16 2009 - 00:21:26 CDT


Dear AMBER ,
thank you Shaowen!

I have given this at the end of my script , but still
i have the same problem
sander.MPI is running and the out put is not printed

i dont know how to slove this
regards
balalji
UOM

> From: shaowen.hu-1_at_nasa.gov
> To: amber_at_ambermd.org
> Date: Wed, 15 Apr 2009 12:56:07 -0500
> Subject: RE: [AMBER] help- regarding - TMD
>
> 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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