RE: [gmx-users] qasi-harmonic entropy calculation
Hi Pedro, I am using 4565.9 as a conversion factor. I dont see any problem unless any condtion I needed to satisfy during the simulation. Simulation gave the result what I had expected. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 8:57 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Maybe there has been some mistake during your calculations? No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. If you have used your own program to calculate entropy double check units conversion stuff. Regards. Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calculating covariance? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 1:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] qasi-harmonic entropy calculation
Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] qasi-harmonic entropy calculation
Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, The CVS head version of g_anaeig computes these values as well. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] qasi-harmonic entropy calculation
Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calculating covariance? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 1:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] qasi-harmonic entropy calculation
Hi David, Thanks for your information and I will have a look CVS head version. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 18/10/2007 4:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, The CVS head version of g_anaeig computes these values as well. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] qasi-harmonic entropy calculation
Maybe there has been some mistake during your calculations? No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. If you have used your own program to calculate entropy double check units conversion stuff. Regards. Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calculating covariance? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 1:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
