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>>
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>>>
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
<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:
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.ivche...@gmail.com
<mailto:olga.ivche...@gmail.com>
<mailto:olga.ivche...@gmail.com
<mailto:olga.ivche...@gmail.com>>
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<mailto:olga.ivche...@gmail.com>>>
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<mailto:olga.ivche...@gmail.com>>>>>
Thank you very much.
best,
Olga
2011/2/21 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>>>
<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 <mailto:jalem...@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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