Olga Ivchenko wrote:
So I used mindist for a certain group of molecules which is surrounded
by water. I got plot number of contacts versuc sumulation time.
According to what I see in a distance < 0.6nm at certain frame there
are on average 150 contacts.
Actually how the programm calculates the number of contacts, if someone
knows what is a creteria that a certain contact is formed?
Is is a certain distance.
Exactly as the title of the output says, a contact exists if any two atoms of
the chosen index groups are within 0.6 nm. You can change the distance with
g_mindist -d.
-Justin
best,
Olga
2011/2/21 Olga Ivchenko <olga.ivche...@gmail.com
<mailto:olga.ivche...@gmail.com>>
Thank you very much.
best,
Olga
2011/2/21 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
g_mindist -on (with suitable index groups) should also do the trick.
-Justin
Erik Marklund wrote:
Or g_hbond -contact. Undfortuntely there are still issues
with g_hbond at the moment. Version 4.0.x seem to work better.
XAvier Periole skrev 2011-02-21 11.37:
g_dist
On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
Dear Gromacs Users,
I would like to know if there is in gromacs an
option how to calculate how many contacts has a
certain atom i(n a molecules of interest) with water
during the whole MD simulations (or at each step of MD).
Please could you advice me on this?
best,
Olga
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Justin A. Lemkul
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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