hello Justin Thank you for your advice, that was really fruitful.
can you kindly tell me how to visualize the molecule which is appearing or disappearing (lamda 0 to 1, lamda 1 to 0 respectively)? moving forward i am interested in calculating free energy of reacting mixtures so could you please tell me how to make a files and how to move forward? Swapnil On Wednesday, 13 August 2014 6:00 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 8/13/14, 12:05 PM, Swapnil Kate wrote: > hello justin, > > i used g_bar -b 100 -f lamda_0/dhdl.xvg -o -oi -oh > With a single input file there's nothing to do. You need to provide all data files (from all of the lambda values) to g_bar. See my tutorial for details. -Justin > swapnil > > > On Wednesday, 13 August 2014 4:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > On 8/13/14, 11:19 AM, Swapnil Kate wrote: > > hello, > > > > I am trying to generate free energy of solvation using g_bar gromacs tool, > > > > i have carried out all steps given in manual for solvation energy, but >when i > am trying to use g_bar command it shows 'nothing to calculate'. > > > > what can be the possible errors because i am not getting correct values? > > > > > You probably issued the command wrong, but since you haven't provided us with > your exact command, there's nothing else to suggest. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu <mailto:jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > > ================================================== > > -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
