[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.

Alan


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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588


More information about the gromacs.org_gmx-users mailing list