AMBER Archive (2003)

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

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Jul 24 2003 - 12:35:21 CDT

First of all there is a line missing from your input at the end:
&rst iat=0, &end
I believe with AMBER7 this is necessary.
What I am also doing is start with a TEMPI=10.0 and not 0.0 ...so far no
problems for me with the temperature.
Assuming that this is an equilibration step ..I am using a tautp=0.2 for
equilibration and 2.0 for production runs....
How is the temperature profile looks like???.
For me looks like the nmropt=1 does not work and the &wt is not read!
But I might be wrong
Hope this helps,
vlad

sd233_at_georgetown.edu wrote:

>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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