AMBER Archive (2003)

Subject: Re: AMBER: TEMP is not reaching 300K

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Thu Jul 24 2003 - 12:35:03 CDT

1) tell us how you equilibrated
2) give the first few energy outputs from the sander output file.

----- Original Message -----
From: <sd233_at_georgetown.edu>
To: <amber_at_scripps.edu>
Cc: <sd233_at_georgetown.edu>
Sent: Thursday, July 24, 2003 1:06 PM
Subject: AMBER: TEMP is not reaching 300K

> Dear AMBER USERS:
>
> I am trying to do dynamics on protein in an explicit water molecules at
> constant pressure,with Waterbox size is 16A.
>
> Also I gave the option to control the TEMP. i.e. not to allow it go
> beyond 300K.
>
> With this I have two problems
>
> 1. TEMP increase is sudden and its reaching beyond 300K.
>
> My INPUT is like below:
>
> __________________________________________________________
>
> imin = 0, nmropt = 1,
>
> ntx = 1, irest = 0, lastrst=6000000, ntrx
> = 1,
>
> ntxo = 1, ntpr = 1, ntrx = 1, ntwr
> = 500,
> iwrap = 0, ntwx = 100, ntwv = 0, ntwe
> = 1,
> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat= 0,
>
> temp0 = 300.0, tempi = 0.0, heat = 0.0, ig = 71277, dtemp =
> 5.0, tautp = 2.0,
> ntt = 1, ntf = 2, ntb = 2, igb =
> 0, nsnb = 5,
> ipol = 0, gbsa = 0,
> dielc = 1.00000, cut = 9.00000, intdiel = 1.00000,
> scnb = 2.00000, scee = 1.20000,
>
> ibelly = 0, ntr = 0,
>
> nstlim = 10000, nscm = 1000, nrespa = 1,
> t = 0.00000, dt = 0.00100, vlimit = 20.00000,
>
> ntp = 1, plevel = 1,
> pres0 = 1.00000, comp = 44.60000, taup = 0.20000,
>
> ntc = 2, jfastw = 0,
> tol = 0.00005,
> &end
> &wt type='TEMP0', istep1=0, istep2=6000,
> value1=0.0, value2=300.0, &end
> &wt type='TEMP0', istep1=6001, istep2=10000,
> value1=300.0, value2=300.0, &end
> &wt type='END' &end
>
> __________________________________________________________________
>
> Could anyone will help me out,
>
> Thanks
> Sincerely,
> Sivanesan.D.
>
>
>
> D.Sivanesan, Ph.D.
> Dept. of Oncology,
> Lombardi Cancer Center,
> Georgetown University, DC 20057
>
>
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