[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 
> this.
> Thanking you,
> Regards,
> Monika

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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