Gavin, I recall mentioning gen_vel=no with temperature coupling as a
possible problem a while ago (the problem is that the initial forces
become initial velocities and then those get scaled up and what you
have are velocities and not temperatures -- read about the flying ice
cube problem).
O.K Chris
Thanks for all your help. I am actually considering removing the
thermostat all together seeing as my system is quite small.
I have also started using gen_vel = yes (no matter how much I think my
system is in equilibrium). One quick question (perhaps its silly). When
you say the initial
velocities are not taken from the .gro as far as I know. You can get
them from the .trr if you also use a .edr.
If you want to check, then do a run for only 1 ps and save your .edr
every timestep. Then run g_energy and look at the temperature.
I am not sure that a constant energy
Dear Chris and Justin
I ran a simulation for two water molecules (100 ns). It only took 5
minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel
=yes, and gen temp =600 (using Nose Hoover). This produced a histogram
with one main peak. I then took the final configuration from
Hi all
I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.
Pull group natoms pbc atom distance at start reference at t=0
07236
1
Gavin Melaugh wrote:
Hi all
I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.
Pull group natoms pbc atom distance at start reference at t=0
072
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi all
I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.
Pull group natoms pbc atom distance at start reference
Thanks Justin
Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all
Gavin Melaugh wrote:
Thanks Justin
Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
Gavin Melaugh wrote:
O.K thanks anyway
I saw the plots you posted during a conversation with Chris, but I'll ask the
obvious anyway: have you watched the trajectories for any of the problematic
windows? It didn't seem like you had two metastable states, but maybe having a
look at the
Justin
I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them again in more detail and post back.
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
O.K thanks anyway
Gavin Melaugh wrote:
Justin
I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them again in more detail and post back.
Plotting the pullx.xvg file(s) may be useful,
I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Justin
I have looked at the movies but it's very hard to tell what's going
Gavin Melaugh wrote:
I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file
That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference group, then
displacement (dX,dY,dZ) of
For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the
Gavin Melaugh wrote:
For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus)
O.K thanks Justine I'll look at these files and see if there is any
weirdness.
Just to make sure that there are no cut-off artefacts. If I set the
cut-offs to zero as in the following mdp file; that does mean that I am
considering all electrostatic and LJ interactions between the molecules?
and
Gavin Melaugh wrote:
O.K thanks Justine I'll look at these files and see if there is any
weirdness.
Just to make sure that there are no cut-off artefacts. If I set the
cut-offs to zero as in the following mdp file; that does mean that I am
considering all electrostatic and LJ interactions
I have seen this before, and there are a few possible reasons, but I'm
still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). It's
really hard to help you when we have to guess what the problem looks
like... or perhaps you
chris.ne...@utoronto.ca wrote:
I have seen this before, and there are a few possible reasons, but I'm
still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
It's really hard to help you when we have to guess what the problem
Hi Chris
Yeah I posted the histograms a few days ago as Justin said. Did you get
the link?
Gavin
chris.ne...@utoronto.ca wrote:
I have seen this before, and there are a few possible reasons, but I'm
still waiting to see that histogram with two peaks
Justin
In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.
Cheers
P.S I have plotted the
Gavin Melaugh wrote:
Justin
In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.
You have
O.K Thanks
My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that ignore the box (from manual) was implemented.
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Justin
In regard to my query
you can post a step by step from the beginning where you copy
and paste absolutely all of your commands (e.g. paste the *exact*
grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
the last line in your starting .gro file.
Chris.
-- original message --
[gmx-users] pbc atom
Gavin Melaugh wrote:
O.K Thanks
My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that ignore the box (from manual) was implemented.
Indeed.
How many atoms are in your system? How well-conserved is
There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
O.K
all of your commands (e.g. paste the *exact*
grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
the last line in your starting .gro file.
Chris.
-- original message --
[gmx-users] pbc atom
Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Aug 24 17:19:45 CEST 2010
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[gmx-users] pbc atom
Gavin Melaugh gmelaugh01 at qub.ac.uk
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Hi Chris
Yeah I posted the histograms a few days ago as Justin said. Did
Dear Gavin:
What happens if you replace your reference group by a single water
molecule and your pulled group by a single water molecule and run the
2.35 nm simulation again. Do you get the same two-peaked histogram?
What about if you use a system with a single water for the reference
Gavin Melaugh wrote:
There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies
I would think it possible, even
Hey,
directly. I think you want this (assuming that cols 5,6,7 give you the
dx,dy,dz, which I believe that they do):
cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}'
my.data
Nothing directly harmful of course, but why using three programs for
this? awk will do
Tsjerk,
Two reasons. First, I simply don't understand awk as well as you do.
Second, I think that breaking it down into simpler commands linked by
pipes is better for teaching. If somebody needs help to combine 3 cols
into a vector distance, then they may copy and paste your solution to
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