AMBER Archive (2005)

Subject: Re: AMBER: difference of energy in sander and nmode in amber 7

From: sebnem (sebnem_at_mercury.chem.pitt.edu)
Date: Wed Aug 17 2005 - 12:51:15 CDT


Hi,
Thanks a lot for your suggestion, but i need to use either ibelly or ntr
in nmode, in order to have something consistent with sander. I need nmode
for second derivative calculation. So i have to find a way to bring nmode
and sander to the same place. Please help me!
thanks in advance,
sebnem

> I think the belly option is implemented differently in nmode and in
> current versions of sander. This means that some terms that would be
> fixed are eliminated from nmode but not from sander.
>
> Try to run without the belly option to see if this helps clear things
> up.
>
> ...good luck...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

Sebnem Essiz

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu