Dear GMX user,
I want to calculate the bonding energy between between two specific atoms.
If it is possible, please help me.
Cheers,
Dhana
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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
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
On 16/03/11, C.Y. Chang chiayun.ch...@gmail.com 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
[
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
On 14/03/11, C.Y. Chang chiayun.ch...@gmail.com 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
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
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
Hi!
I want to calculate energy from GROMOS96-GB/SA. What command should
be used?
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simon sangma wrote:
Hi!
I want to calculate energy from GROMOS96-GB/SA. What command
should be used?
g_energy
-Justin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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