Thanks I'll give PCA a try! Natalie
________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: 21 November 2011 12:04 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape On 21/11/2011 10:36 PM, Natalie Stephenson wrote: > I have performed force pulling experiments on a protein with both Gromacs MD > simulations and experimentally with AFM. The problem I'm facing with the > data is the difference between the loading rates of the two approaches. For > the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a > much lower loading rate of 1 x 10^-8 N/s. > > I was told at a conference I attended that there was a way of constructing a > 'potential energy landscape' which would be able to use this to remove the > loading rate differences. However, I did not get a chance to find out how > this was possible. I understand how g_sham works, however, I'm not sure what > - in this case - the input would be in order to construct such a 'potential > energy landscape'. Any insight into how I would be able to create this ... or > any other ideas on how I would be able to somehow relate the simulation > output to experimental data dispite the loading rate differences would be > GREATLY appreciated!! Forget the misleading term "potential energy landscape". It seems nobody here knows how your contact thinks constructing a plot of free energy as a function of two observables will address the loading rate difference. Justin described how g_sham works. Your analysis may suggest the right observables for use with g_sham, or you may wish to use essential dynamics (aka principal component analysis) to determine these algorithmically. Check out manual 8.10 if so. Mark > > Thanks once again!! > Natalie > > ------------------------------------------------ > Natalie Stephenson, B.Sc > PhD Research Associate > > Manchester Interdisciplinary Biocentre > 131 Princess Street > Manchester > M1 7DN > x65816 > ------------------------------------------------ > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] > Sent: 14 November 2011 12:15 > To: jalem...@vt.edu; Discussion list for GROMACS users > Subject: RE: [gmx-users] Potential Energy Landscape > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: 21 October 2011 13:25 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Potential Energy Landscape > > Natalie Stephenson wrote: >>> Hi Justin (and gmx-users), >>> >>> I've been looking into using g_sham for the free energy landscapes, however >>> I'm not sure what variables I should plot ... could I just use the g_energy >>> (potential) outputs to produce the energy landscape?? Other examples I've >>> seen using g_sham have done quite in depth eigenvector projections before >>> plotting them using g_sham. >>> >> The free energy of potential energy is probably not a meaningful quantity ;) >> >>> What inputs would I require in order to determine how loading rate an >>> increased loading rate on the simulation would change the force results? >>> >>> I know I'm probably being completely dumb but my use of maths has been >>> sporadic to say the least in the last 7 years ... so getting back into it is >>> proving more confusing! >>> >> You haven't provided a lot of detail about what you're doing, what you've >> measured, or what you hope to achieve. In general, one plots two variables >> (one >> on each axis), and g_sham calculates a free energy based simply on the >> probability of occurrence of these values. For instance, for protein folding >> experiments, often the RMSD relative to the known structure is one variable, >> and >> something else like native contacts or hydrogen bonds is plotted as the other >> variable. The free energy surface is then generated as a function of >> intramolecular association and similarity to a known structure. >> >> -Justin >> > Sorry it's taken so long to reply to this one, experimental issues dragged my > focus! > I have performed force pulling experiments on a protein with both Gromacs MD > simulations and experimentally with AFM. The problem I'm facing with the > data is the difference between the loading rates of the two approaches. For > the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a > much lower loading rate of 1 x 10^-8 N/s. > > I was told at a conference I attended that there was a way of constructing a > 'potential energy landscape' which would be able to use this to remove the > loading rate differences. However, I did not get a chance to find out how > this was possible. I understand how g_sham works, however, I'm not sure what > - in this case - the input would be in order to construct such a 'potential > energy landscape'. Any insight into how I would be able to create this ... or > any other ideas on how I would be able to somehow relate the simulation > output to experimental data dispite the loading rate differences would be > GREATLY appreciated!! > > Thanks once again!! > Natalie > >> Natalie >> >> ------------------------------------------------ Natalie Stephenson, B.Sc PhD >> Research Associate >> >> Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN >> x65816 ------------------------------------------------ >> >> ________________________________________ From: gmx-users-boun...@gromacs.org >> [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul >> [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS >> users Subject: Re: [gmx-users] Potential Energy Landscape >> >> Natalie Stephenson wrote: >>> I was recently told in passing that it would be possible to construct a >>> 'potential energy landscape' from the simulations I have performed. This >>> way I could remove any loading rate differences between simulations and >>> experimental force experiments I've been performing ... however I cannot >>> find anywhere in which this is mentioned. >>> >>> The only thing close I could find that was close was the free energy >>> landscape using g_anaeig under the Dihedral PCA >>> (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca >>> >>> <http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca>) >>> however, I'm not sure this is what I'm looking for. >>> >>> Does anyone know where I would be able to find out / read more about how to >>> create potential energy landscapes from my simulation outputs? >>> >> g_sham produces free energy landscapes for any variables plotted against one >> another. >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee >> Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | >> (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== -- 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 > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- 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
