AMBER Archive (2009)

Subject: RE: [AMBER] reg-TMD

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (shaowen.hu-1_at_nasa.gov)
Date: Wed Apr 29 2009 - 15:56:07 CDT

You may try adding nmropt=1 in your script, and change tgtrmsd to 16.0. I encountered a same problem before.

Best,
Shaowen

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan
Sent: Tuesday, April 28, 2009 11:16 PM
To: amber forumnew
Subject: RE: [AMBER] reg-TMD

Dear Dr . Carlos Simmerling ,

I am sorry i may not be clear , to explain,

I am giving my script below ,
if not the force has to be changed , then what shall i have to do ,
i am not able to get your words , i am sorry .
------------------------------------------------------------------
&cntrl
  imin = 0, ntx=1, nstlim=3000000,
  irest =0,
  ntb = 2,
  pres0 = 1.0,
  ntp =1 ,
  ntxo = 1,
  ntx =1,
  tempi =300.0,
  ntc=2,
  ntf = 2,
  nscm = 0,
  ntwr = 50
  ntpr = 50,
  ntwx = 50,
  ntwv =50,
  ntwe = 50,
  ntt = 3,
  gamma_ln = 1.0,
  temp0 = 300.0,
  dt = 0.001,
  scee=1.2,
  cut =8.0,
  itgtmd=1,
  tgtrmsd =0.0 ,
  tgtmdfrc =0.016,
  tgtfitmask= ":1- 76"
  tgtrmsmask= ":1- 76"
 /

&wt
        TYPE='TGTRMSD', istep1=1, istep2=3000000,
        value1 =16.0, value2 = 1.0,
  / &wt
   type="END"
-------------------------------------------------------
The current Rmsd value stays at 7.1 itself and its not going down towards 0

regards
balaji
UOM

> From: carlos.simmerling_at_gmail.com
> Date: Tue, 28 Apr 2009 13:48:18 -0400
> Subject: Re: [AMBER] reg-TMD
> To: amber_at_ambermd.org
>
> using the force to control the transition rate is probably not useful,
> change the target value instead. it looks like this is what you are doing,
> so I am not sure what you mean by it not working. is the rmsd value not what
> you requested?
>
>
> On Tue, Apr 28, 2009 at 11:23 AM, balaji nagarajan <balaji_sethu_at_hotmail.com
> > wrote:
>
> >
> > Dear Amber ,
> >
> > Thank you
> > Dr. Ccarlos Simmerling
> > and Shaowen
> >
> > I have solved my problem , now the Tmd in explicit water in going
> > good ,
> >
> > the problem is with the parameter file , it has been corrected
> >
> > i need another clariffication regarding the
> > weighting option
> >
> > I gave a force and after some time the rmsd is not changing its going at a
> > constant value
> > if i give the greater force i can not view the transition clearly because
> > it moves from one structure to the other in
> > a rapid manner ,
> >
> > is there any option to change the weight after some time during the run
> > like changing both force and the weighting option ,
> > /
> > &wt
> > TYPE='TGTRMSD', istep1=1, istep2=1000000,
> > value1 = 16.00, value2 = 8.00,
> >
> > /
> > &wt
> > TYPE='TGTRMSD', istep1=1000000, istep2=2000000,
> > value1 = 8.00, value2 =1.00,
> >
> >
> > /
> >
> > or is there any way to fix this problem .,
> >
> >
> > balaji
> > UOM
> >
> >
> >
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