Mark Abraham wrote:
OK I have some confirmation of a possible bug here. Using 4.0.4 to do
reruns on the same positions-only NPT peptide+water trajectory with the
same run input file:
a) compiled without MPI, a single-processor rerun worked correctly,
including zero KE and temperature at
Hi,
I can fix, but I am currently very busy, so it might take some time.
Berk
Date: Fri, 24 Apr 2009 17:56:56 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Identical energies generated in a rerun calculation
... but ...
Mark Abraham wrote:
Hi,
I think you can replace all state- by state_global- within { } after the if
statement
on line 929 of md.c.
Then I think it should work for serial, PD and DD.
Mark, could you test if this works and report back?
Thanks,
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE:
Respectable Experts
I am very grateful to Justin.
Yes I have defined the atom OB with its mass in the ffgmx.atp file. I have also
defined the residue OMOL in ffgmx.rtp file that I am using.
Thank you
___
gmx-users mailing list
Sunil Thapa wrote:
Respectable Experts
I am very grateful to Justin.
Yes I have defined the atom OB with its mass in the ffgmx.atp file.
I have also defined the residue OMOL in ffgmx.rtp file that I am using.
Any particular reason for using ffgmx? It is deprecated; the newer Gromos96
Dear Mark
After doing second step of inflategro i.e compression step when I
did the enery minimisation with nstep-1 in parameter file it
terminated after 1547 steps and written that -
Converged to machine precision,
but not to the requested precision Fmax 2000
Double precision
Hi ,
I can not fully understand the picture of parameter of pull geometry of
cylinder.
Who can say something about it, Thanks in advance.
Thanks in advance.
-
pull geometry
cylinder
Designed for pulling with respect to a layer where the reference COM is
Hello GMX-people
I am trying to locate the source code files regarding free energy
perturbation (FEP) calculations. Does anyone have an idea?
regards,
--
Murat Cetinkaya, PhD
Max-Planck-Institute for Metals Research
Protein Mechanics and Evolution Group
Bioquant BQ0031, Universitaet
a
grep -rl -e FEP -e dvdlambda *
in the gromacs source directory will show you these files.
Carsten
On Apr 24, 2009, at 4:33 PM, murat cetinkaya wrote:
Hello GMX-people
I am trying to locate the source code files regarding free energy
perturbation (FEP) calculations. Does anyone have an
Dear All,
I just found that there is a problem when I extract the density
of water from my Gromacs simulations.
When I used g_density to get the water density from .trr
trajectory file, the density plot looked normal. But when I used trjconv
to convert the .trr to .gro file,
Dear All,
I just found that there is a problem when I extract the density
of water from my Gromacs simulations.
When I used g_density to get the water density from .trr
trajectory file, the density plot looked normal. But when I used trjconv
to convert the .trr to .gro file,
On Fri, Apr 24, 2009 at 4:13 PM, nitu sharma sharmanit...@gmail.com wrote:
Dear Mark
After doing second step of inflategro i.e compression step when I
did the enery minimisation with nstep-1 in parameter file it
terminated after 1547 steps and written that -
Converged to
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