AMBER Archive (2000)

Subject: Re: unable to extract trajectory of MD simulation with sander_classic

From: David Konerding (dek_at_konerding.com)
Date: Wed Jun 28 2000 - 10:57:48 CDT

Minmin Wang writes:
>Dear Amber Users,
>
>I used the following script to do MD simulation with Sander_Classic
>(AMBER6):
> &cntrl
> imin=0,
> ntx=5, irest=1,
> cut =9.0,
> ntt=4,temp0=20.0 dtemp=0.0, tautp=1.0,
> ntb=0, ntc=2, tol=0.000001,
> ntpr=100, ntwx=5,
> ntr=0,
> nstlim=4000,
> scee=1.2,idiel=1,
> dt=0.002,
> &end
>
>but I can not retrieve the output coordinate sets. The output mdcrd file
>contains a blank line. Is this a known bug or how can I overcome it?
>Thanks,

This is likely the problem:
http://www.amber.ucsf.edu/amber/doc6/manual_updates.html

p. 262: NTWXM is now the minimum time for which coordinate snapshots will
be dumped, i.e. there will be no snapshots recorded for the first NTWXM
steps; after that, coordinates will be dumped every NTWX steps. Similarly
for NTWVM and NTWEM. The intent is that snapshots might not be needed
for an initial equilibration period.

you probably want to set ntwxm to 0.

(it's a silly change and a non-intuitive one)

Dave