Hi,
This problem is not very strange at all.
Different CPU's have different efficiencies for different types of code.
In this case the Opteron and new Xeon have measurably different
(although probably not more than 20%) relative performance
for particle-particle and PME interactions.
Also, your
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 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 in that case
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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Hello together,
i have a problem with msd. i simulate a melt of chain molecules
consisting of 116 united atoms per chain. then i copy the box n
times in x,y,z directions, repeat simulations and get a slightly
different msd curves:
in the time range between 1 ps and 10 ps it flattens out decrea
Hi all
I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell.
I have just discovered that if I add the variable "GROMACS" with variable value
"...path\GROMACS" in the
System - Advanced - Environment Variables - User variables section of the
control panel and also add t
George Tsigaridas wrote:
Hi all
I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell.
OK, so *use* the Cygwin shell... there are much easier ways of setting
environment variables for the Cygwin shells than through the XP control
panel (though, rarely, this can be n
Hi,
g_msd calculates the msd for molecules, not for atoms.
I guess that would explain the result when you half the chain length.
It might also explain the box size effects, since whole chains will
still have a reduction in MSD due to periodiciy with a box of 3 Rg.
If you run g_msd without -mol y
OK Mark. But at least, I wonder if the use of the command prompt is going to
make easier the application of MPI in a PC network running Windows XP (see
also my previous message). What's your opinion?
Thanks
George
- Original Message -
From: "Mark Abraham"
To: "Discussion list for G
Hey,
I tried everything you suggested and a couple more things and still it
is not possible to get a reasonable speed
for the pulled groups (always way beyond the 0.01nm/ps set in the mdp
file and mostly containing some high frequence patttern probably related
to pbc). (I tried: constraint, pbcato
Hi,
The only thing I suggested was using pull_start=yes,
otherwise you will start at a "random" distance and you will have enormous
forces.
Did you try that?
Do you have a rectangular or a triclinic box?
Berk
> Date: Thu, 3 Sep 2009 18:00:44 +0200
> From: alexander.h...@mytum.de
> To: gmx-us
Hi Justin,
I think it is the minimization issue. I did steep for 2000 steps, and it
works thereafter for the mdrun, for this structure.
Thank you very much!
Regards,
Stone Gao
--
From: "Justin A. Lemkul"
Sent: Tuesday, September 01, 2009 4:35 P
Dear all,
In the martini tutorial there is a approach of martini + ElneDYN . In the
tutorial they provided me a script which converts the cleaned pdb structure
to CG structure of protein. I compiled the script using g77 (as they
recommended) and then I am trying to make the CG structure of 1BL8 pro
sunny mishra wrote:
Dear all,
In the martini tutorial there is a approach of martini + ElneDYN . In
the tutorial they provided me a script which converts the cleaned pdb
structure to CG structure of protein. I compiled the script using g77
(as they recommended) and then I am trying to make
Hello all.
I have tried to perfomed some simulations about protein dynamics including
one copper ion, close from the protein, by Gromacs/CPMD. However, I get
some problems during CPMD simulation.
In the *.mdp file I added the following:
---
Dear all,
I've tried to simulate a membrane system with POPC and protein following
Justin's tutorial. The system was minimized with 2 stages. First using
restraint on everything accept water for 1 SD steps:-
Steepest Descents converged to Fmax < 1000 in 1785 steps
Potential Energy = -1.6945709
Hi
The 3.3.3 and 4.0.5 version were installed under =>
*
source /usr/gromacs/4.0.5/setup.sh
source /usr/gromacs/3.3.3/setup.sh*
*The 4.0.5 version is currently the default one.*
I want to compare the computation results from 4.0.5 version and 3.3.3
version.
So, I write the
*source /usr/gromacs/3
Chih-Ying Lin wrote:
Hi
The 3.3.3 and 4.0.5 version were installed under =>
*
source /usr/gromacs/4.0.5/setup.sh
source /usr/gromacs/3.3.3/setup.sh*
I've no idea what these scripts are, but the correct procedure is to
follow the advice about GMXRC here:
http://oldwiki.gromacs.org/index.php/In
Bing Bing wrote:
Dear all,
I've tried to simulate a membrane system with POPC and protein following
Justin's tutorial. The system was minimized with 2 stages. First using
restraint on everything accept water for 1 SD steps:-
Steepest Descents converged to Fmax < 1000 in 1785 steps
Potential E
Hi
The system is "one lysozyme + water " running on 16 nodes.
After => Energy minimization of the solvated systemRelaxation of solvent and
hydrogen atom positions: Position restrained MDThen, the error was shown.
---
Program mdrun_mpi, VERSION 4
Chih-Ying Lin wrote:
Hi
The system is "one lysozyme + water " running on 16 nodes.
After => Energy minimization of the solvated systemRelaxation of solvent and
hydrogen atom positions: Position restrained MDThen, the error was shown.
---
Progr
Hi
No matter
pbc = no or pbc = xyz
Energy Minimisation is required with particle decomposition.
That is, mdrun -pd is required.
Why?
Thank you
Lin
___
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Hi
I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under
16 nodes.
Simply, lysozyme.pdb + water.
There is no problems (errors) with 3.3.3 version.
However, with 4.0.5 version, the same lysozyme pdb file with the same
simulation condition.
except mdrun -pd with minimisation
Chih-Ying Lin wrote:
Hi
I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under
16 nodes.
Simply, lysozyme.pdb + water.
There is no problems (errors) with 3.3.3 version.
However, with 4.0.5 version, the same lysozyme pdb file with the same
simulation condition.
except mdru
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