Re: [gmx-users] Problem sasa 3.2.1 vs 3.3.2
Thank you for your answer. Today I send the email directly to David and Erik. I hove they could help me. I will post the answer in the list. Thank you. Cheers, Anthony On Thursday 18 September 2008 03:59:29 pm Tsjerk Wassenaar wrote: Hi Anthony, It's not even that different. The order is swapped (the colors) and the most notable difference is that the noise is higher in the newer version. The running averages will probably give very similar results. Still interesting to know what happened to the noise. The answer is probably in the source (and may be in a head belonging to a developer). Cheers, Tsjerk On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz [EMAIL PROTECTED] wrote: Hi users: Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa analysis I observe differences in the sasa values between the two versions. The total sasa seems to be same in the two graphs but the hydrophobic and hydrophilic looks very different (see attached pictures). What could be the problem? Which version will be the best for analysis? Cheers, Anthony ___ 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] Problem sasa 3.2.1 vs 3.3.2
Hi users: Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa analysis I observe differences in the sasa values between the two versions. The total sasa seems to be same in the two graphs but the hydrophobic and hydrophilic looks very different (see attached pictures). What could be the problem? Which version will be the best for analysis? Cheers, Anthony attachment: Untitled.png___ 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] Problem sasa 3.2.1 vs 3.3.2
Hi Anthony, It's not even that different. The order is swapped (the colors) and the most notable difference is that the noise is higher in the newer version. The running averages will probably give very similar results. Still interesting to know what happened to the noise. The answer is probably in the source (and may be in a head belonging to a developer). Cheers, Tsjerk On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz [EMAIL PROTECTED] wrote: Hi users: Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa analysis I observe differences in the sasa values between the two versions. The total sasa seems to be same in the two graphs but the hydrophobic and hydrophilic looks very different (see attached pictures). What could be the problem? Which version will be the best for analysis? Cheers, Anthony ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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
