Olga Ivchenko wrote:
Yes, I want to plot number of contacts agains tempreture. But in
thermodynamics when temperature changes the pressure changes or the
volume. But in my system volume and pressure is the same at different
tempretures. Just I wanted ti be sure if it is ok to do like this even
if the pressure is the same at different tempretures.
I guess this all depends on how "different" your temperatures are. If the
pressures do not change substantially, then there is no problem, since the
system density is reasonably similar.
-Justin
best,
Olga
2011/2/23 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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> <mailto: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>>
<mailto: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>>
<mailto: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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Virginia Tech
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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