AMBER Archive (2009)

Subject: Re: [AMBER] slope

From: Jio M (jiomm_at_yahoo.com)
Date: Sun Nov 15 2009 - 22:42:52 CST

Dear Sir,

I am using following input file

&cntrl

  nstlim=1050000,

  ntt=3, gamma_ln=5,

  scee=1.2,

  ntpr=500, pencut=0.1,

  nmropt=1,

  vlimit=10,

  ntb=0,dt = 0.0005,cut=999,ntwx=500

/

 &wt type='TEMP0', istep1=0,istep2=140000,

   value1=300.0, value2=2000.0

 /

 &wt type='TEMP0', istep1=140001,istep2=200000,

   value1=2000.0, value2=2000.0

 /

 &wt type='TEMP0', istep1=200001,istep2=340000,

   value1=2000.0, value2=1000.0

 /

 &wt type='TEMP0', istep1=340001,istep2=480000,

   value1=1000.0, value2=2000.0

 /

 &wt type='TEMP0', istep1=480001,istep2=620000,

   value1=2000.0, value2=1000.0

 /

 &wt type='TEMP0', istep1=620001,istep2=760000,

   value1=1000.0, value2=2000.0

/

 &wt type='TEMP0', istep1=760001,istep2=900000,

   value1=2000.0, value2=1000.0

/

 &wt type='TEMP0', istep1=900001,istep2=1050000,

   value1=1000.0, value2=300.0

 /

 &wt type='END'

 /

--- On Sun, 11/15/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Subject: Re: [AMBER] slope {no reply}
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Sunday, November 15, 2009, 7:07 PM

for (1) it all depends on how you set the thermostat temp0, which
thermostat and what coupling constant. no way to predict your data
without that.

On 11/15/09, Jio M <jiomm_at_yahoo.com> wrote:
>
>
>
>
> Dear Amber users,
>
>
>
> 1) I am performing annealing and want to plot temp vs steps graph ..is
> it neccessary that temp vs steps plot should give
> linear rise or fall of graph of slope 45 degree or it should be linear
> what so ever slope may be ?
>
>
>
> 2) same query as before.. can we solubilize the system with single molecule
> instead of box solvent
>
>
>
> please suggest
>
>
>
> thanks and regards;
>
> Jiomm
>
>
>
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
Stony Brook University           E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================

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