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 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 other than g_saltbr gromacs tools be used for that
(E,g g_dist ) ?
James
2013/2/3 Justin Lemkul <jalem...@vt.edu>:
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 with the groups defined in the index
file so I should just select all residues that I need in that file,
shouldnt it ? Also doest it possible to select pairs of residues
Yes.
placed in the sequence on the distant sites ? (e.g by selecting only
pairs within some range of n1 and n2+k where k>n1+10)
I don't understand what you mean. tpbconv will only take one index
group
for zeroing charges, so I don't understand how such a relative
scheme would
work for all cases.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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