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-differ
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
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 te
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 eve
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 sa
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
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 whi
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
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
Thank you very much.
best,
Olga
2011/2/21 Justin A. Lemkul
>
> 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 bett
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
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
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).
Pleas
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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