[gmx-users] Re: Tcoupl default setting
Thank you Mark for your response, In carrying out the test you recommended I realised that I had set the integrator to sd, in such a case the tcoupl parameter is ignored. This explains my well behave temperature in the absence of setting a tcoupl option. When I wrote the input file originally (months ago) I must have known what I was doing but then we live, we learn, we forget. Regards Charlie -- 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] Tcoupl default setting
Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t and ref_t has a default thermostat also been turned on by default and if so which one, or have I not performed an NPT but rather an NPE simulation with my apparent well behaved temperature just being coincidental. Needless to say there is no mention of tcoupl in the output file. Regards Charlie. -- 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] Tcoupl default setting‏
Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t and ref_t has a default thermostat also been turned on by default and if so which one, or have I not performed an NPT but rather an NPE simulation with my apparent well behaved temperature just being coincidental. Needless to say there is no mention of tcoupl in the output file. Regards Charlie. Apologies for possible double posting -- 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] Amb2gmx
Dear all, Lennard Jones radius parameters are converted between gromacs and amber with the conversion factor (2**(5/6))/10 in the amb2gmx script. While I understand that the 10 takes care of the Angstrom to nanometers conversion I do not understand the origin of the 2 to the power of 5/6. I would like to know how it arises? Thanks Charile -- 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
