[gmx-users] maximum number of molecules

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 19 02:37:21 CEST 2002

On Thu, 18 Apr 2002, Rainer Boeckmann wrote:

>> >a few weeks ago there was a question concerning the maximum number of atoms
>> >allowed in GROMACS (2^31-1). I now realized that the maximum number of molecules
>> >is limited to about 100.000 - not in mdrun but one gets problems in preparing
>> >large systems using editconf. editconf may write wrong coordinates and/or
>> >velocities when converting files.
>> No it works. Just try it. The largest runs in gromacs we have done here
>> are 450,000 atoms.
>hmm...not in my case. editconf writes wrong coordinates when for example converting
>a g96-file into a pdb-file. In contrast it writes correctly a g96-file from the tpr.
>grompp does wrong when writing a tpr-file from a g96, correct when using a pdb-file.
>I think that this depends on the number of molecules (more than 100,000 in my case),
>not on the number of atoms and appears only when converting a g96-file, but I tested
>not all combinations...
I see, pdb file might be a problem, but gro and g96 work.

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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