AMBER Archive (2008)

Subject: Re: AMBER: hybrid remd imaging

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Mar 24 2008 - 10:59:24 CDT

you're right, that doesn't seem to be working correctly.
can you send me directly your sander input? also do you have
anything else in the system except the 1 peptide and water?

On Mon, Mar 24, 2008 at 11:51 AM, Geoff Wood <geoffrey.wood_at_epfl.ch> wrote:

> Dear Amber Community,
> I am curious about the imaging done in hybrid remd calculations.
>
> If I use ptraj commands (see below) to post process a trajectory then the
> imaged trajectory looks like what one would expect (see attached picture).
> However, if I look at the stripped restart file then the imaging seems to
> be a bit strange (see the other attached picture). Could anyone comment on
> this?
>
>
> ptraj commands:
>
> *trajin coords*
> *center * mass origin*
> *image origin center*
> *solvent byname WAT TIP3*
> *closest 350 :mask first*
> *trajout coords.strip nobox*
>
> Thanks,
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
sanderRestart.jpeg
ptrajout.jpeg ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu