RE: [gmx-users] free energy landscape question
Yes, that is an interesting question. I don't know the answer, but is there any way to get the numerical values of the matrix from Gromacs tools that produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is another candidate. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Andrei Neamtu Sent: 23 June 2010 01:00 To: gmx-users@gromacs.org Subject: [gmx-users] free energy landscape question Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines plots of the surface Many thanks, Andrei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] free energy landscape question
On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote: Yes, that is an interesting question. I don't know the answer, but is there any way to get the numerical values of the matrix from Gromacs tools that produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is another candidate. probably the easiest is to look at the code and print out the matrix before it's sent to the xpm plotting routine. you can also convert the xpm afterwards, but I guess the data then gets quantized. cheers, marc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] free energy landscape question
Dear Andreas and Marc, Thanks for your reply. I am not familiar with the gromacs programming code and so I am trying to build myself the FEL. I can generate the hisotgram of the number of states from the projection along principal component 1 and 2 (PC1 and PC2) using SigmaPlot but here I am stucked! I think that I have to compute the free energy with the formula G = - kT ln(Pi/Pmax) where Pi is the probability of the state i (determined py a certain pair of values of PC1 and PC2) and Pmax is the maximum probability. But for certain there are regions in the principal component plane with probabiliy zero which constitutes singularities for the above formula (infinite energy). Any ideas? Many thanks, Andrei On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink lens...@bigre.ulb.ac.be wrote: On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote: Yes, that is an interesting question. I don't know the answer, but is there any way to get the numerical values of the matrix from Gromacs tools that produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is another candidate. probably the easiest is to look at the code and print out the matrix before it's sent to the xpm plotting routine. you can also convert the xpm afterwards, but I guess the data then gets quantized. cheers, marc -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] free energy landscape question
On Wed, 23 Jun 2010, Andrei Neamtu wrote: Dear Andreas and Marc, Thanks for your reply. I am not familiar with the gromacs programming code and so I am trying to build myself the FEL. I can generate the hisotgram of the number of states from the projection along principal component 1 and 2 (PC1 and PC2) using SigmaPlot but here I am stucked! I think that I have to compute the free energy with the formula G = - kT ln(Pi/Pmax) where Pi is the probability of the state i (determined py a certain pair of values of PC1 and PC2) and Pmax is the maximum probability. But for certain there are regions in the principal component plane with probabiliy zero which constitutes singularities for the above formula (infinite energy). Hi Andrei, You can simply assign to those regions a very high energy value (e.g., 100RT) that works as +infinite. In practice, this doesn't matter, since you will always use an energy cutoff much lower than that when plotting or projecting your landscape. From my experience, you should also pay attention to the choice of bin size and the eventual use of smoothing methods, especially if you are thinking about going to 3D or higher-dimensional histograms. We ended up using kernel density estimates instead of histograms (http://dx.doi.org/10.1021/jp902991u). Have a nice landscaping, Antonio Any ideas? Many thanks, Andrei On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink lens...@bigre.ulb.ac.be wrote: On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote: Yes, that is an interesting question. I don't know the answer, but is there any way to get the numerical values of the matrix from Gromacs tools that produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is another candidate. probably the easiest is to look at the code and print out the matrix before it's sent to the xpm plotting routine. you can also convert the xpm afterwards, but I guess the data then gets quantized. cheers, marc -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] free energy landscape question
Dear Antonio, thank you. I think I got the idea. I need to use a cut-off for the probability: for all the probabilities lower than a certain value I assign to them that (lower) value so the energy will be constant. Thanks, Andrei On Wed, Jun 23, 2010 at 8:49 PM, bapti...@itqb.unl.pt wrote: On Wed, 23 Jun 2010, Andrei Neamtu wrote: Dear Andreas and Marc, Thanks for your reply. I am not familiar with the gromacs programming code and so I am trying to build myself the FEL. I can generate the hisotgram of the number of states from the projection along principal component 1 and 2 (PC1 and PC2) using SigmaPlot but here I am stucked! I think that I have to compute the free energy with the formula G = - kT ln(Pi/Pmax) where Pi is the probability of the state i (determined py a certain pair of values of PC1 and PC2) and Pmax is the maximum probability. But for certain there are regions in the principal component plane with probabiliy zero which constitutes singularities for the above formula (infinite energy). Hi Andrei, You can simply assign to those regions a very high energy value (e.g., 100RT) that works as +infinite. In practice, this doesn't matter, since you will always use an energy cutoff much lower than that when plotting or projecting your landscape. From my experience, you should also pay attention to the choice of bin size and the eventual use of smoothing methods, especially if you are thinking about going to 3D or higher-dimensional histograms. We ended up using kernel density estimates instead of histograms (http://dx.doi.org/10.1021/jp902991u). Have a nice landscaping, Antonio Any ideas? Many thanks, Andrei On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink lens...@bigre.ulb.ac.be wrote: On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote: Yes, that is an interesting question. I don't know the answer, but is there any way to get the numerical values of the matrix from Gromacs tools that produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is another candidate. probably the easiest is to look at the code and print out the matrix before it's sent to the xpm plotting routine. you can also convert the xpm afterwards, but I guess the data then gets quantized. cheers, marc -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista -- -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] free energy landscape question
Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines plots of the surface Many thanks, Andrei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] free energy landscape question
Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines plots of the surface Many thanks, Andrei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
