Re: AMBER: problem with temperature weights

From: Carlos Simmerling <>
Date: Fri, 07 Oct 2005 12:55:12 -0400

does the output say that is has read the weight changes?
read the top portion (up to step 1 energies) carefully as
it should verify the weight changes assigned.
also you might need tighter coupling (smaller tautp)
to enforce the ramping at the rate you want.

Manish Datt wrote:

>hi all
>i`m trying to run md on a protein-dna complex with following input
>dynamcis 300000
> &cntrl
> imin=0, irest=0, ntx=1, nstlim=300000, dt=0.001,
> drms=0.01, ntb=0, cut=999, ntpr=10, ntwx=100, ntwr=100, ntt=3,
> igb=1, ntr=0, nmropt=1, tautp=1.5, gamma_ln=1, tempi=0, temp0=30
> /
> &wt
> type='TEMP0', istep1=0, istep2=10000,
> value1=0.0, value2=10.0
> &end
> &wt
> type='TEMP0', istep1=10001, istep2=20000,
> value1=10.0, value2=20.0
> &end
> &wt
> type='TEMP0', istep1=20001, istep2=30000,
> value1=20.0, value2=30.0
> &end
> &wt
> type='END'
> &end
>now the problem is that the temperature crossess 10k after 0.27ps, while
>as per weights given the temperature should reach 10k after 10ps.
>moreover identical output was obtained when no weights were specified.
>i`m absolutely clueless on how to interpret my results. is theresomething
>that i`m missing out?
>any guidance on how to control temperature change would be
>Manish Datt
>Research Scholar
>Bioinformatics Centre
>Institute of Microbial Technology
>Sector 39A, Chandigarh-160036
>The AMBER Mail Reflector
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Received on Fri Oct 07 2005 - 18:53:00 PDT
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