On 11/6/12 10:42 PM, Ali Alizadeh wrote:
Dear All users
I used OPLS ff for my system and I did not break my bonds,
When i use gromos96 45a3 after minimizing my bonds break(i can see
em.gro) but i do not get any errors in this step
Bonds do not break during MD. Probably what you're seeing is a periodicity
effect.
After md production i get this error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
Lots of information on the Gromacs website:
http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps.
...and also in the list archive.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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