[gmx-users] Energy Calculation

2012-01-07 Thread Dhanachandra Singh
Dear GMX user, I want to calculate the bonding energy between between two specific atoms. If it is possible, please help me. Cheers, Dhana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Energy calculation

2011-03-17 Thread C.Y. Chang
Hi, "Every charge group must be a subset of an energy group or fully disjoint from it." Does it mean that I could not set up the HBD and HBA in the ligand at the same time, but the HBD in ligand and HBA in lipid bilayer could be calculate? or Each atoms in the ligand must belong to the disjointed

Re: [gmx-users] Energy calculation

2011-03-16 Thread Mark Abraham
On 16/03/11, "C.Y. Chang" wrote: > Hi, > > I try to calculate the Hbond in the ligand and remove the duplicate atoms in > the .ndx file dumped from g_hbond. > This is the contents in the .ndx file. > > [ HBD ] >  17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 > > [ HBA ] >  17

Re: [gmx-users] Energy calculation

2011-03-16 Thread C.Y. Chang
Hi, I try to calculate the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond. This is the contents in the .ndx file. [ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412 1

Re: [gmx-users] Energy calculation

2011-03-14 Thread Mark Abraham
On 14/03/11, "C.Y. Chang" wrote: > Hi, > > I try to calculate hydrogen bond (HB) energy. > The g_energy does not have this term. > And I find the g_hbond function in Gromacs. > But the HB energy calculation is not in g_hbond. > There's good reasons for this. How would you define the "HB ener

[gmx-users] Energy calculation

2011-03-14 Thread C.Y. Chang
Hi, I try to calculate hydrogen bond (HB) energy. The g_energy does not have this term. And I find the g_hbond function in Gromacs. But the HB energy calculation is not in g_hbond. Therfore, I also try to dump the .ndx file including the HB_donor, HB_acceptor and HB_system from g_hbond, and perfro

Re: [gmx-users] Energy calculation problem with molecule leaving the box

2011-02-03 Thread Mark Abraham
On 4/02/2011 1:05 AM, Gordan Horvat wrote: I'm doing molecule dynamics of a calixarene in a acetonitrile box with pbc, energy groups defined and npT constant. When I extract interaction energies with g_energy from edr file I expect them to be pretty much constant because I see no significant co

[gmx-users] Energy calculation problem with molecule leaving the box

2011-02-03 Thread Gordan Horvat
I'm doing molecule dynamics of a calixarene in a acetonitrile box with pbc, energy groups defined and npT constant. When I extract interaction energies with g_energy from edr file I expect them to be pretty much constant because I see no significant conformational changes or changes in distance

[gmx-users] Energy calculation

2010-06-21 Thread Thanasis Koukoulas
hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is  ; VARIOUS PREPROCESSING OPTIONStitl

Re: [gmx-users] Energy Calculation

2010-02-25 Thread Justin A. Lemkul
simon sangma wrote: Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? g_energy -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

[gmx-users] Energy Calculation

2010-02-25 Thread simon sangma
Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe