AMBER Archive (2005)

Subject: RE: AMBER: restart file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 05 2005 - 16:15:49 CDT

> You're right, I got **** in my restart files, I will use IWRAP=1 from
> those points of simulations.
> I'm thinking another way to solve this problem: can one run a short
> minimization then a good restart file is created?
> Thanks for the quick answer!

I'm not sure about this. First of all running the minimisation would mean
you get a restart file with no velocity information in it. Hence it isn't
really a continuation of your MD. Secondly it will only help if it reimgages
the coordinates. What happens, at least in periodic boundary simulations is
that only the original molecules are kept track of. Hence you can get a
water molecule that can difuse a long way away from the central box.
Eventually the coordinates of this water molecule are too large to fit in
the formatted space in the restart file. At this point the program simply
writes *'s to this space. This then makes the restart file useless. Hence
your best option is to always set IWRAP=1 so only the coordinates of central
image are written or alternatively take a good restart file (before th *
problem arrives) and reimage it manually using ptraj before proceeding with
your next step of MD.

Since people are now routinely running many NS md simulations perhaps we
should look to make the restart file widths larger and/or implement a binary
restart file format.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be ready every day, and should not be used for urgent or sensitive issues.

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