Hey James, Have you thought about the physical relevance of your results?
Cheers, Tsjerk On Wed, Apr 11, 2012 at 12:01 PM, James Starlight <[email protected]> wrote: > Tsjerk, > > Thank you for suggestions! > > > Indeed the hight temperature ( I'm using 700K) which I use for enhansing > sampling rate resulted in destabilisation of the secondary structure. > > To prevent this I've used two slightly different aproaches based on the > restraint. But in both cases I've used slightly soft restrains with > fs=10-200. > > The first aproach is the ussage of the posres applied on each backbone atom > with fc=10-50. I've tested case with fc=50 and found that such restrains > were very hight. I've not noticed any conformation sampling of my protein ( > rmsd of backbone < 0.3 nm) during 10ns of such simulation. So I've decided > to test a case with fc=10 ( under calculation) > > The second approach is the application of the harmonic distance restrainse > wich I've applied on each backbone atom pair in the CUTOFF radius of 1.0 nm. > The Rc value was chosen because of my protein is the 7 buddle of alpha > helices so this aproach could be usefull but exactly value for R have been > chosen empirically. I've selected deviation value wich are equal to 1\2 of > cutoff radius = 1.5 nm. I have not realise whaat I could obtain yet from > this because I'm not quite sure about coccect values of such disres. > > > James > > 11 апреля 2012 г. 13:35 пользователь Tsjerk Wassenaar <[email protected]> > написал: >> >> Hey :) >> >> I'd say a protein should be loosing structure at 700K. Can't even say >> the force field is wrong there, even though it hasn't been >> parameterized for such temperatures for certain. You'd have to check >> with experiments. >> Trying to do high-temperature simulations is fine. But trying to do >> high temperature simulations to get results that match a room/body >> temperature ensemble is completely bogus. If you aim to use this >> approach for enhanced sampling, you're in for some serious >> reparameterization. Part of the deal may indeed be adding >> long(er)-range distance restraints. However, the force constants to >> use will increase with temperature, and with very high temperatures >> the force constants may end up so high that they give rise to fast >> oscillations, which will require using a smaller time step. >> >> Just my 2 cents... >> >> Tsjerk >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
