[gmx-users] GROMACS problem

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 25 20:52:51 CEST 2002

On Thu, 25 Jul 2002, alexander yakovenko wrote:

>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.
Charge groups can not be larger than 32 atoms (we use an integer as
bitmask somewhere). If you use PME you can certainly make your charge
groups smaller, it wil lnot affect the coulomb interactions.

>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 ?
It could also be a problem of poor equilibration, that shows up earlier
when using constraints than with bonds. It can however also be a topology

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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