Tsjerk,
As Justin already has noticed there were lot of examples of implementation of the high temperature aproach to increase conformation sampling. This could be usefull because of short time-scale of typical MD trajectory and hight energy barriers of the adjacent energy-minimums wich could correspond to the functional-relevant conformations. So the main reason of such stimulations in to dicrease such barriers to promote transitions to the functional-relevant states conformations Finally I can sample the output of such simulation and compare this resulted conformations with the experimental data. If I obtain good similarity this may indicate about efficiency of such aproach On other hand such simulation could result in some non-native conformations due to the non-native condtions. So the artificial restrains like as the distance restrains within native conformation ( obttained by NMR for instance) could be usefull-aproach to keep the system in the native-like conformations while enhansing sampling of the native-like structures via rising of temperatures. So combinations of such tricks could give physical-relevant results partly couldn't it ? However I suppose that the main disadvantage of such aproach is the non-physical intermediate states produced by non-native transitions pathways wich could arrise from such simulation. James 11 апреля 2012 г. 18:09 пользователь Tsjerk Wassenaar <[email protected]>написал: > 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 >
-- 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
