Dear Gromacs users,
At the moment I have some doubt on my run input .mdp file.
I simulated a protein structure in water and I used parameters as following in
my mdp file:
title= MD simulation of xxx
;Preprocessor
cpp = /lib/cpp
;Directories to include in the
Hi Emanuel,
Anything small can cause trajectories to diverge, it's chaos. The
machine on which is run can make the difference. This is also covered
in the list archives.
;Temperature coupling
tcoupl = nose-hoover
tc-grps = protein NA+ CFP SOL
tau_t = 0.1 0.1
Hi Tsjerk,
I ran my job on the same machine and made exactly the same inputstructure and
inputfile.
What does chaos mean in your opinion? A computer should do exactly the same
every time you start with the same starting conditions on the same machine.
I have to couple my ligand seperately
Well, unfortunately it doesn't. Numerical differences are introduced
here and there for different resasons. On some machines the registers
have more bits than you'd normally fit into a float or double, and hence
give higher precision. If those registers are pushed to the stack, then
the
Hi Justin,
I'm still trying to figure out what happened with my ligand.
Meanwhile, I have another question: I can't figure out how to calculate an
average structure in gromacs.
And does g_rmsf calculate the average structure automatically?
Thanks again
Carla
On Tue, Feb 16, 2010 at 5:44 PM,
Dear Erik,
I still have some trouble to understand.
Could you give me a more detailed answer why I get two different
trajectories on the same machine? It should have the same registers and
numerical chaos should be exactly the same in that case.
Bests,
Emanuel
Erik Marklund 02/17/10 10:05
Hi Carla,
Justin's recipe should've worked. As he suggested, maybe the ligand is
not with the protein. You can check by multiplying your system with
genconf:
genconf -f in.pdb -o out.pdb -nbox 2 2 2
If the ligand is with the protein, one copy will be located in one of
the copies of the protein.
Dear Gromacs users,
I have another question.
Does that mean that I cannot compare my simulations if I have performed just
2 different jobs?
How many runs should I then start to compare my chaotic trajectories?
Thanks in advance.
Bests,
Emanuel
Emanuel Peter 02/17/10 10:19 AM
Dear Erik,
Now that depends entirely on what you're interested in. The
thermodynamics of your different trajectories should not differ much,
which is one of the reasons that the chaotic nature of MD ios not much
of a problem in most cases.
Erik
Emanuel Peter skrev:
Dear Gromacs users,
I have another
The times when registers are pushed to the stack may happen at different
points in the calculations in different runs, so the bonus accuracy
may be lost at different times. As I mentioned, a hardware interrupt may
(will) force such an event, and this may be due to some external
trigger, such
- Original Message -
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Date: Wednesday, February 17, 2010 20:46
Subject: Re: [gmx-users] Same starting structure but different trajectories
To: gmx-users@gromacs.org
Dear Gromacs users,
I have another question.
Does that
Date: Wed, 17 Feb 2010 03:12:57 +1100
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Power6 @ 4.7 Ghz vs Xeon E5472 @ 3.00GHz
On 17/02/10 03:06, pim schravendijk wrote:
Dear Gromacs users,
I have been installing Gromacs on a Power6 4.7 GHz with
Hi,
Gromacs, including the MPI version, is completely deterministic,
except for, if I recall correctly, two algorithms.
One is PME with fftw as the FFT library. FFTW does timings of different
algorithms
and uses the fastest one, the results will depend on the exact load of the
machine
during
Ah, I noticed just now that the Xeon model is in the subject line.
So it is not a Nehalem Xeon. Then the difference is somewhat larger than I
expected.
Maybe using fortran could help a bit.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Power6 @ 4.7 Ghz vs Xeon
Thank you Tsjerk,
but one more question:
if I do the following: g_rmsf -f a.xtc -s b.tpr -o rmsf.xvg -ox average.pdb
-n c.ndx
does gromacs claculate the rmsf after fitting to b.tpr or to average.pdb?
if I want it to calculatefluctuations between the position of
particle i and the time-averaged
Hi,
I would like to calculate the density maps for the water inside a pore that has
a cilindrical shape, but not the water outside it, that is also present in the
box.
I don´t understand vey well the options of g_densmap -amax and -rmax. With
-amax I define the maximun axial distance from the
Dear GROMACS users,if I want to use table defined potential for nonbonded interactions I have to do so for all pairs between different grops or is there a possibility to specify just one kind lets say BH potential by tables and to use wdvtype=cut-off for LJ interactions. It seems to me that this
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