Sir, You are right..I exactly mean the same as you interpreted....now I am clear. Thanks a lot for your reply... On Fri, Jul 8, 2011 at 13:26, felmer...@uchile.cl <felmer...@uchile.cl>wrote:
> Hey, > > I agree it was unclear, but i guess he meant that he has a crystal > structure with two molecules in the asymmetric unit where he knows that the > protein is a monomer in solution. Otherwise the question does not even make > sense as you pointed out. > > If it is indeed the asymmetric unit thing, then of course starting from any > of the two structures will give different resultsas they are two different > startinf points. However, on the long term all the system properties should > converge on the average. Anyways, you should obtain very similar results > from any of the two structures. > > regards > > Felipe > > ----Mensaje original---- > De: mark.abra...@anu.edu.au > Fecha: 08-jul-2011 3:44 > Para: "Discussion list for GROMACS users"<gmx-users@gromacs.org> > Asunto: Re: [gmx-users] which chain to select for MD simulation > > > On 8/07/2011 4:52 PM, bipin singh wrote: > > Hello, > > > > My protein have two identical chains A and B and the backbone rmsd > > between the two chains is 0.33A. > > My problem is that how to select(on what basis) one chain out of the > > two for md simulation, whether the selection of one of the two > > chains(A or B) will make any differences to the final results. > > Step back. Does it even make sense to use only one? Dimers are usually > that way for a reason. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ----------------------- *Regards,* Bipin Singh
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