AMBER Archive (2002)

Subject: Re: belly and EWALD in amber7

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Sun Nov 10 2002 - 16:25:31 CST

Dear Jian
Its not a big problem. It means that energies are not right since
interactions between frozen atoms are not supposed to be calculated but
are at least partially calculated by PME. However the forces should be ok.
Its still ok to use belly + pme for equilibration. Don't try to interpret
energies or energy differences however involving pme with belly option.
hope this helps
tom
On Sat, 9 Nov 2002, Zhang Jian
wrote:

> Dear AMBER users,
>
> I use belly to do a equilibration of a protein in
> water, then got a warning in my output file, it reads,
> =======================
> Warning, Although EWALD will work with belly (for
> equilibration), it not strictly correct!
> =======================
> does this warning matter? how to correct it?
>
> here is my min.in file
> =======================
> minimize structure
> &cntrl
> imin=1, ibelly=1, ntr=0, ntb=2, ntc=1, ntf=1,
> ntp=1, pres0=1.0, taup=0.2,
> ntx=1, ntpr=1, ntwr=1,
> maxcyc=10, ncyc=20,
> &end
> Belly minimization, only allow water to relax
> RES 37 1186
> END
> END
> ======================
>
>
> Thank you in advance.
>
> Regards,
> Jian Zhang, Dr
>
>
>
>
>
> =====
> Jian Zhang, Dr
> Institute for Biophysics
> Nanjing University
> 22 Hankou Road, Nanjing 210093
> P. R. China
> Tel: 86-25-3594476
> Fax: 86-25-3595535
>
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