AMBER Archive (2005)

Subject: Re: AMBER: restart file

From: Harianto Tjong (harianto_at_mailer.sb.fsu.edu)
Date: Tue Jul 05 2005 - 15:49:16 CDT

Dr. Walker & Dr. Simmerling,
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!
Best regards,
Harianto.

Ross Walker wrote:

>I suspect that your system is diffusing too far such that the coordinates no
>longer fit in the space allocated in the restrt file. Check the restrt file,
>you will probably see lines with ***'s in them. If you are not interested in
>measuring diffusion coefficients then you can set IWRAP=1 in your input
>file. This will wrap all coordinates back to the central box rather than
>tracking the original molecule. This way you shouldn't come accross this
>problem.
>
>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 |
>
>
>

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