Olga Ivchenko wrote:
If I am using g_mindist to calculate the number of contacts at different
tempretures of the system. I am thinking if it will make sense because
the system has a periodic boundary conditions and the pressure at each
tempreture is defined manually and is the same. The only parameter in
the script which should be different at different tempretures is
pressure. Please could you advice me on this?
So you want to plot contacts as a function of temperature? I don't see any
problem with doing that. On what do you need advice?
-Justin
best,
Olga
2011/2/21 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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> <mailto: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> <mailto: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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Virginia Tech
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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