AMBER Archive (2002)

Subject: Re: Problem in run

From: Monica Jain (monicdbs_at_iitr.ernet.in)
Date: Sat Nov 09 2002 - 00:52:46 CST

Dear Sir,
your guess is right.I am using AMBER6 and when I used ntt=1, erroe
disappeared.
Should I use ntt=1 for constant preesure equilibration also.
Thank you.

David Case wrote:
>
> On Sat, Nov 09, 2002, Monica wrote:
>
> > I am running DRUG-DNA complex using NMR distances in explicit water.
> > Minimization was done successfullt but when I am running initial
> > equilibration it gave following error
> >
> >
> > Rescaling velocities by 35.16041
>
> This is pretty scary! My best guess is that you are using amber6 (?)
> and that you set ntt=4 (?) That will only work for an equilibrated
> system...I recommend ntt=1 for intial equilibration.
>
> (Actually, I don't know of any situation where ntt=4 is a desirable option;
> that's why it has been removed from current versions of sander.)
>
> Of course, my guesses could be way wrong (basically, I searched the code
> for your error message....). If you have problems in the future, please
> give more information about what you did.
>
> ...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================