Re: [gmx-users] surface tension
Hi Pri, Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm) serge priyanka srivastava wrote: Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] channel size calculation between active site lid
You can use program called HOLE: http://d2o.biop.ox.ac.uk:38080//, it can calculate the pore profile of your channel. raja wrote: Hi all, I followed center of mass (COM) between lids region (two loops covering the entrance of active site) during simulation to see its action of opening and closing. Normally COM varies for all simulation of my protein (Wild and its mutant variant) is between 17A to 20A. Now I want to find out the average opening size (Pore or channel size) during simulation through which the substrate believed to reach the active site. How to do it either within or outside of gromacs? With thanks! B.Nataraj -- Serge Yefimov University of Groningen Department of Applied Physics Micromechanics of Materials Nijenborgh 4, 9747 AG Groningen The Netherlands tel: +31-50-3634835 fax: +31-50-3634886 e-mail: [EMAIL PROTECTED] --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: Can not open file: topol.tpr
can you read the tpr file with, say, editconf, from the same directory? serge -- Serge Yefimov University of Groningen Department of Applied Physics Micromechanics of Materials Nijenborgh 4, 9747 AG Groningen The Netherlands tel: +31-50-3634835 mob: +31-6-49935870 fax: +31-50-3634886 e-mail: [EMAIL PROTECTED] --- Guillem Plasencia wrote: I ran mpirun options mdrun more options from inside the folder where topol.tpr was, so unless i have to specify the path explicitly i think it should have to see that file. any other ideas? Thank you very much ! -- Guillem Plasencia ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
