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

[Justin A. Lemkul]

Olga Ivchenko wrote:
Thank you Justin,
Because the pressure is how often molecules collide with each other, 
what has a relation to number of contacts  between two molecules.

Clearly, but do you have any real data that suggest (based on pressure or 
anything else) that explains the non-difference in your data?  You said "I think 
it has something to do with the pressure."  How so?  What is the average 
pressure in each system?  Are the differences significant or insignificant?  On 
the microscopic scale, pressure is a relatively useless quantity.  But if you're 
using pressure coupling and the same ref_p in both cases, you have your answer - 
there is no difference in pressure.

-Justin

best,
Olga

2011/2/25 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>



    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.

        Please could you advice me on this?


    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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@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 <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>>>>




                  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
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                         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
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                                Thank you very much.
                                best,
                                Olga

                                2011/2/21 Justin A. Lemkul
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                                    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
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                                    Department of Biochemistry
                                    Virginia Tech
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                                    jalemkul[at]vt.edu <http://vt.edu>
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                             (540) 231-9080

                                                 
        http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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                         --     ========================================

                         Justin A. Lemkul
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                         Virginia Tech
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                         jalemkul[at]vt.edu <http://vt.edu>
        <http://vt.edu> <http://vt.edu>
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                  Justin A. Lemkul
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           Justin A. Lemkul
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    -- 
    ========================================

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
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    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
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Department of Biochemistry
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Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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