[gmx-users] GROMACS problem

[alexander yakovenko]

Dear all,
I work with nonproteion molecules using gromacs, and have some problems.
Does anybody know is the gromacs MD simulation crash if the number of charge groups in rtp file more than 32 ? I have about ten examples of such crashing, but it may be the problem of my molecules type. This crush took place in MD simulation only, but not in energy minimization.
The second question is about mechanism of crashing. If I have the constrain all-bonds string in my mdp file and the signed bond energy and lenght in rtp and in MD, one of the molecule's atom "fly out".  Is this a problem of toplogy or it is the gromacs problem ?
Thank you.

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
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E-mail: yakovenko_a at ukr.net