AMBER Archive (2007)

Subject: Re: AMBER: problem with Thermodynamic Integration

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Sep 19 2007 - 11:45:47 CDT

Dear Martin,

Are you using Amber 9? In order to do TI Calculation in Amber 9, you need
to use sander.MPI, meaning that you need to compile AMBER in parallel.

Best,

On Wed, 19 Sep 2007, Martin Stennett wrote:

> I'm trying to run thermodynamic integration, and have followed the manual pretty much to the letter so far.
> The only problem I've run into is that when I try to run
>
> prun -n 2 sander -ng 2 -groupfile 0.tp3.TI.in
>
> I get the error message:
>
> >mdfil: Error unknown flag: -ng
> >usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> >[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
> >Consult the manual for additional options
>
> It strikes me as odd that the flag is unknown, but also in the list of known flags... should they be in a specific order??
>
> Regards,
> Martin Klefas-Stennett
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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