[gmx-users] how many contacts has a certain atom at MD
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 23 14:21:39 CET 2011
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 <jalemkul at vt.edu <mailto:jalemkul at 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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at 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.ivchenko at gmail.com
> <mailto:olga.ivchenko at gmail.com>
> <mailto:olga.ivchenko at gmail.com
> <mailto:olga.ivchenko at gmail.com>>
> <mailto:olga.ivchenko at gmail.com <mailto:olga.ivchenko at gmail.com>
>
> <mailto:olga.ivchenko at gmail.com
> <mailto:olga.ivchenko at gmail.com>>>>
>
>
> Thank you very much.
> best,
> Olga
>
> 2011/2/21 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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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> -- ========================================
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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 <http://vt.edu> <http://vt.edu>
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> -- ========================================
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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 <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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