[gmx-users] Simulating a 282 atom molecule. How do I split it into parts?

Alan alanwilter at gmail.com
Mon Jan 6 11:54:54 CET 2014

Well, allow me this suggestion. Consider using
http://q4md-forcefieldtools.org/ to get the right charges, then update
these charges in the mol2 file and run acpype with “-c user” option. For a
quick test, you can use “-c gas”, which would give you charges via
gasteiger method.


On 5 January 2014 22:07, Jonathan Saboury <jsabou1 at gmail.com> wrote:

> I have this molecule I want to simulate:
> http://pastebin.com/raw.php?i=7bsWKjU3
> I have tried using acpype on the whole thing to obtain the needed .itp and
> .gro, but it takes a couple days to finish and I get errors because I do
> not have enough memory.
> I was wondering if splitting this molecule into parts, much like how
> proteins are split into amino acid sections, would be a feasible way to
> simulate this molecule. I haven't seen any tutorials on this, so not sure.
> I could split the molecule into the bowl shapes, the n-hexanes, and the
> n-pentane linker. Or if that would not be the correct way, how would you do
> it?
> My question is how would the input sections deal with the bonds between
> sections? For example, if I had a ethane and wanted to split it into two
> methyl pieces, would I make the input .pdb's as CH3's? I.E.:
> http://pastebin.com/raw.php?i=jhwcYbAM
> And more importantly, how would I link these together in the .gro file?
> (assuming it is the .gro file)
> Thank you, your help is very much appreciated!
> -Jonathan
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

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