Re: AMBER: restart file

From: Harianto Tjong <>
Date: Tue, 05 Jul 2005 16:49:16 -0400

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,

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
>All the best
>|\oss Walker
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel: +1 858 784 8889 | EMail:- |
>| | PGP Key available on request |

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Jul 05 2005 - 22:53:00 PDT
Custom Search