AMBER Archive (2008)

Subject: Re: AMBER: wrapping a restart file

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Jun 30 2008 - 11:34:54 CDT

Tom Cheatham or someone else can undoubtedly better comment on this than I
can. BUT, while ptraj can wrap a restart file, if you are doing constant
pressure runs, I have had big grief trying to still end up with a continuous
trajectory for analysis after the wrap, as things can get wrapped around
inconsistently internally to sander/pmemd vs. externally in ptraj (and there
is the issue of the changing boxsize). There are a bunch of options, but I
have ultimately found it simpler to just either leave wrapping on all the
time in the simulation code, or to do a 1 step wrap (which I essentially
drop out of the trajectory). I think lots of folks just leave wrapping on
all the time because then the restart never overflows. You do pay a slight
performance penalty for this, but it should be small as the frequency of
restart writing and trajectory writing is relatively low (that said, I am
such a performance freak that I monitor my restarts for overflow and do the
1 step wraps myself (you can use vi to look for say 7..\. in the restart -
then you know you are 2/3 of the way to overflow). Also, continuous
wrapping does mess up certain types of analysis.
Regards - Bob Duke

----- Original Message -----
From: <fatima.chami_at_durham.ac.uk>
To: <amber_at_scripps.edu>
Sent: Monday, June 30, 2008 10:40 AM
Subject: AMBER: wrapping a restart file

> Dear Amber's users,
>
> can Ptraj wrap a restart file... I need to create a pdb file and then
> load this
> into Leap to modify it and generate another configuration.
>
> best wishes
> Fatima
>
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