AMBER Archive (2005)

Subject: Re: AMBER: problem with temperature weights

From: Manish Datt (mdatt_at_imtech.res.in)
Date: Fri Oct 07 2005 - 23:50:07 CDT

dear carlos
the output has indeed read the weight changes but strangely it has not
read in the tautp flag.
what should be done to rectify this?

Manish Datt
Research Scholar
Bioinformatics Centre
Institute of Microbial Technology
Sector 39A, Chandigarh-160036
India.

On Fri, 7 Oct 2005, Carlos Simmerling wrote:

> 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
> >highly
> >appreciated.
> >
> >regards,
> >
> >Manish Datt
> >Research Scholar
> >Bioinformatics Centre
> >Institute of Microbial Technology
> >Sector 39A, Chandigarh-160036
> >India.
> >
> >
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