[gmx-users] how many contacts has a certain atom at MD
Olga Ivchenko
olga.ivchenko at gmail.com
Fri Feb 25 11:35:00 CET 2011
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?
best,
Olga
2011/2/23 Justin A. Lemkul <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>>
>>
>>
>>
>>
>> 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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>> -- ========================================
>>
>> 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> |
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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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