[gmx-users] g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). Why? Furthermore, I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.html -- gmx-users mailing listgmx-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] Help g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.html -- gmx-users mailing listgmx-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] Help g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.html -- gmx-users mailing listgmx-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] Pressure coupling
Hello everyone. I want to know if can be applied pressure coupling only in the z direction, allowing the edges x and y simulation box with fixed size. -- gmx-users mailing listgmx-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] viscosity
*On 2013-06-01 17:11, Marcelo Vanean wrote: * > > *On 2013-06-01 02:24, Marcelo Vanean wrote: > > * >> >> *Hello to everyone. In version 4.5.5, calculating the viscosity with the >> command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and >> visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a >> value of zero for viscosity using the Einstein relation. Another question >> in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas >> in >> version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? >> Evidently, there is an inconsistency in these different results. Help me, >> please. >> >> >> * > > *I used the same energy file (ener.edr) and I get this results: > http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. > > * *Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)?* I didn't the pressure autocorrelation. A question: what does this analysis tell me? I posted the energy file here: http://www.4shared.com/file/SSAU1reN/ener.html. -- gmx-users mailing listgmx-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] (no subject)
On 2013-06-01 02:24, Marcelo Vanean wrote: > Hello to everyone. In version 4.5.5, calculating the viscosity with the > command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and > visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a > value of zero for viscosity using the Einstein relation. Another question > in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in > version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? > Evidently, there is an inconsistency in these different results. Help me, > please. > > I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. -- gmx-users mailing listgmx-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] Viscosity
Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. -- gmx-users mailing listgmx-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] Charge groups
Hi. I'm with doubts concerning the charge groups. I am simulating ethylene glycol and the only way of charged groups are neutral is putting all atoms in only one charge group. This is advisable? Is that a problem? What is the greatest number of atoms in a charge group which is recommended? -- gmx-users mailing listgmx-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] Fwd: Rycaert-Bellemans function
Hello to all. I am simulating long-chain alcohols. For the dihedrals, I used Rycaert-Bellemans function. In this case I should delete the pairs from topology? -- gmx-users mailing listgmx-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
