[gmx-users] Dimer simulations using Gromacs
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 26 09:02:59 CET 2007
Monika Sharma wrote:
> Dear All,
> I wish to do some simulations using dimer of protein. I have generated
> .gro file for that. I am able to minimize structure, but when I am
> trying to give it for equilibration run. I am getting error as:
> "Warning: 1-4 interaction between 5786 and 5791 at distance 5.468 which
> is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file"
> On looking the gro file it seems that these atom numbers corresponds to
> two different chains of the dimer. But it is trying to map it as one
> protein molecule instead of two as can be seen from the topol.top file.
> [ molecules ]
> ; Compound #mols
> Protein 1
> FAD 1
> NAD 1
> FAD 1
> NAD 1
> SOL 123000
> My question is that is it normal for gromacs to read dimer as single
> unit in .gro file. Or do I need to make some modifications in .gro and
> .top file to make it read as two entities. Suggestions are required for
> Thanking you,
please check whether pdb2gmx connected the two chains by inspecting your
topology. in that case you have to label the the chains differently
before running pdb2gmx.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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