So lets say that I delete the first frame from the trajectory in which some
atoms might have been outside the box. Everything should be within the box
once the simulation starts (from the second frame onwards)? So the procedure
should work if the reference structure is the second frame? I have
Lets make it clear. I can not tell you if the atoms in the second
frame are in the
box or not! You have to visualize it!
Honestly it is not in the first frame I can not see how it would in
the second!
You have to build a reference structure that has the bilayer in one
piece, then
the
For quite a long time I had the feeling that trjconv doesn't resolve all
situations. Following the very recent discussion between Roland Schutz
and Tsjerk, I'm not sure there is an immediate solution. Ad hoc
approaches such as preparation of tpr files from intermediate snapshots
were useful for me
Hi Berk,
Shorter tau_p? I thought you suggested 5.0 or 10.0 ps ?
On Wed, Sep 2, 2009 at 5:28 PM, Berk Hess g...@hotmail.com wrote:
Hi,
I also just recalled that we have a bug report open since two years already
about drift of the COM:
http://bugzilla.gromacs.org/show_bug.cgi?id=165
But
I meant 3 instead of 30 ps.
I would say 1 ps is too short for systems with a phase with large molecules___
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maria goranovic wrote:
Dear Experts
I had posted this earlier, but the problem was not solved by earlier
suggestions. So am posting again.
I am simulating a POPC bilayer using MARTINI. The simulation ran fine,
but the bilayer drifted towards the edge of the box along the bilayer
normal,
I am not sure how to fix the trajectory that has drifted ...
But if your bilayer drifts even if you use a removal of the COM for
the water and
bilayer separately that means there is problem in the code! And this
should be
fixed.
XAvier.
On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
I will try centering with one of the lipid tail atoms .. that could solve
the problem.
This the way I have specified the comm_groups:
nstcomm = 1
comm-grps = Lipid W
OR
nstcom = 1
comm-grps = system
-Maria
On Wed, Sep 2, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl wrote:
I am not
Hi,
I am 99.99% sure that there is no problem with COM motion removal in Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory
so that the bilayer is at the center
Here are the mdp parameters:
title= POPC
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.030
nsteps = 300
nstcomm = 1
comm-grps = Lipid W
;
your second value for tau_p is missing the . is this a typo?
On Sep 2, 2009, at 4:45 PM, maria goranovic wrote:
Here are the mdp parameters:
title= POPC
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt
Oh dear. That is not good. the missing decimal point in tau_p it is a typo
all right. but it seems i have used it in the simulations too. thank you for
noticing, Xavier.
that forces redoing a lot of simulations.
that said, it should still not impact the center of mass removal anyway?
-maria
It might actually affect the center of mass motion removal,
because you would be scaling your system with 1 +- 1 bit at every step.
This could produce consistent rounding in one direction in single precision,
causing the system to move in one direction.
This is something we should check in
I will change the tau_p values, and report back. This might take more than a
week though.
maria
On Wed, Sep 2, 2009 at 5:16 PM, Berk Hess g...@hotmail.com wrote:
It might actually affect the center of mass motion removal,
because you would be scaling your system with 1 +- 1 bit at every
Hi,
I also just recalled that we have a bug report open since two years already
about drift of the COM:
http://bugzilla.gromacs.org/show_bug.cgi?id=165
But in that case double precision did not change anything, so that does not
seem to be a precision issue.
Here tau_p was 1 ps, but up till now
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