[gmx-users] how many contacts has a certain atom at MD

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 25 12:50:47 CET 2011

```
Olga Ivchenko wrote:
> Regarding my previous question. I performed 2 simulations (minimization,
> NVT, NPT, and that 10ns production run), one with 300K and another with
> 309K. Fir each temperature I calculated how many contacts has my
> molecule with water within a certain distance. But the number of
> contacts at different temperatures is the same. It differs on 0.1. I
> think it has something to do with pressure. I would really like to be
> able to perform simulations that I could get correct different value of
> number of contacts versus temperature.
>
>

I would think the more likely answer is that a difference of 9 K (a 3% change)
is insignificant.  Why do you think the pressure is the reason for the (lack of)
difference?  Can you prove that the pressure is or is not significantly
different in this case?  Values of pressure fluctuate on the order of hundreds
of bar for most systems, so I doubt there is any way to prove that pressure has
any effect, since in most cases, it is a relatively insensitive quantity.

-Justin

> best,
> Olga
>
> 2011/2/23 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     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> <mailto: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
>
>
>            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>>
>         <mailto: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>>>
>                <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
>         <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>
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>                       <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).
>
>                                          best,
>                                          Olga
>
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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> <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> <http://vt.edu>
>         <http://vt.edu> | (540)
>                231-9080
>                   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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>     --
>     ========================================
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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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