Mark Abraham wrote:
Berk Hess 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 for the prompt response.
I ha
On Fri, Apr 24, 2009 at 4:13 PM, nitu sharma 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 machine precision,
>
Anna Marabotti wrote:
Dear All,
I'm trying to perform my first Normal Mode Analysis on a protein of 158
residues, therefore I read the Gromacs
manual searching for the proper way to do it.
I understand that the first step is a deep minimization of my protein, but when
I tried to apply it to my
Hi,
My apologies in advance, I'm aware that this is probably a stupid question...
If I've run a simulation using the umbrella sampling branch of the pull code (gromacs 3.3.1), in which I restrain a small molecule to a membrane, which options must I include when running g_energy to obtain the energy
Zhang Hui wrote:
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 .tr
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, and
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, and
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
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 Heidelberg
Dear All,
I am doing a simulation of aromatic salts interacting with
surfactant micelles of cylindrical geometry, and would like
to get the radial orientation distributions of the surfactant
and aromatic molecules relative to the normal of the cylindrical
micelle surface, or relative to the cent
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
g
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
var
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 listgmx-us
Dear All,
I'm trying to perform my first Normal Mode Analysis on a protein of 158
residues, therefore I read the Gromacs
manual searching for the proper way to do it.
I understand that the first step is a deep minimization of my protein, but when
I tried to apply it to my
system, it failed to rea
Berk Hess 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 for the prompt response.
I had tried something equ
nitu sharma 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 machine precision,
but not to the requested precision Fmax
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 n
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: [
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
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 e
20 matches
Mail list logo
