Hi,
If you don't care about the exact distances, but rather the time the
groups spend within a certain distance, g_hbond -contact can be useful.
Best,
Erik
On Feb 3, 2013, at 6:36 PM, James Starlight wrote:
Justin,
1 )for example I want to select in index file only all asp, glu and
his re
On 2/3/13 12:36 PM, James Starlight wrote:
Justin,
1 )for example I want to select in index file only all asp, glu and
his residues ( I could find selection by residue type only).
What you would do is create a complement to that group - keep all the Asp, Glu,
and His charged and use -zeroq
Justin,
1 )for example I want to select in index file only all asp, glu and
his residues ( I could find selection by residue type only).
2) Than I'd like that gromacs compute dynamics of the distance between
that charge groups (providing only truncated .tpr file as the input)
but only. Could othe
On 2/3/13 1:01 AM, James Starlight wrote:
Justin,
thanks again for suggestions.
I'm not quite sure how I can use tpbconv -zeroq. For example I want to
reduce charges of all amino acids except Asp Glu and His ( to monitor
s.b dynamics between that groups only).
As I understood -zeroq working
Justin,
thanks again for suggestions.
I'm not quite sure how I can use tpbconv -zeroq. For example I want to
reduce charges of all amino acids except Asp Glu and His ( to monitor
s.b dynamics between that groups only).
As I understood -zeroq working with the groups defined in the index
file so I
On 2/2/13 12:18 AM, James Starlight wrote:
Justin,
I suppose that the ussage of the sub-set of trajectories is suitable
when you've already known possible salt-bridge pairs. But that time
I'd like to obtain that information from my trajectory.
E.g I have membrane-embedded protein which is the
Justin,
I suppose that the ussage of the sub-set of trajectories is suitable
when you've already known possible salt-bridge pairs. But that time
I'd like to obtain that information from my trajectory.
E.g I have membrane-embedded protein which is the buddle of
alpha-helixes. I want to examine dyna
On 2/1/13 3:22 PM, James Starlight wrote:
Dear Gromacs users!
I have trajectory from which I want to investigate dynamics of all
possible salt bridges (E.g distance between adjacent + and - charged
residues) of my protein during the simulation
As I understood ussage of g_saltbr -t -sep could
Dear Gromacs users!
I have trajectory from which I want to investigate dynamics of all
possible salt bridges (E.g distance between adjacent + and - charged
residues) of my protein during the simulation
As I understood ussage of g_saltbr -t -sep could be suitable for such
thing but I'm not sure i
9 matches
Mail list logo
