Thank you very much Justin, Stephane.
I found them. Where can I find .mdp parameters related files eg. thermostat
code or electric field?
On Fri, Jun 12, 2015 at 11:27 PM, mah maz wrote:
> hi Justin,
> in the gromacs website i can see different versions, regressiontests and
> xdrs. which one sho
Please, anyone comment on the correct usage of g_spatial.
I need a distribution of a solvation shell around an ion.
Do I choose the solvent as the first group (i.e. all atoms belonging
to the solvent) and the ion as the second group?
:-) g_spatial_mpi (-:
Option
Le 12/06/2015 20:44, Justin Lemkul a écrit :
If you're looking for the source code, download it from the GROMACS
website. Packaged distributions don't include the source.
-Justin
It's simpler than downloading the file, use the "-devel" or "-dev"
package from the officiale repositories, for
On 6/12/15 2:57 PM, mah maz wrote:
hi Justin,
in the gromacs website i can see different versions, regressiontests and
xdrs. which one should i download?
my question is about a code written for each command eg. msd calculation.
where can i find it?
http://www.gromacs.org/Downloads
Pick the G
hi Justin,
in the gromacs website i can see different versions, regressiontests and
xdrs. which one should i download?
my question is about a code written for each command eg. msd calculation.
where can i find it?
thank you!
On Fri, Jun 12, 2015 at 11:06 PM, mah maz wrote:
> dear all,
>
> i want
On 6/12/15 2:36 PM, mah maz wrote:
dear all,
i want to find files that are probably written in C, C++ or fortran format
for commands in gromacs. i tried root/usr/share/gromacs but there are only
a few files, not all of them. note that the version i installed is a rpm
one. where can i find them
dear all,
i want to find files that are probably written in C, C++ or fortran format
for commands in gromacs. i tried root/usr/share/gromacs but there are only
a few files, not all of them. note that the version i installed is a rpm
one. where can i find them?
thanks!
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Gromacs Users mailing li
Dear Andre sir,
Thank you for your reply. I have a problem in the topology file which I
have generated and it is working fine now. Thank you for your support.
Yours sincerely,
*Dr. C.Kumaraswamy Naidu, Ph.D.*
Post doctoral Fellow Bioinformatics,
Department of PMI, School of Medicine,
Universit
On Wed, Jun 10, 2015 at 7:22 PM, Alex wrote:
> Well, I've had a Gigabyte-made OC'd GTX 660 at home (for gaming) for a
> few years, no problems at all.
Note that a bad pixel in games won't ruin the experience, but a bit
flip can easily crash a simulation.
--
Szilárd
> I guess my question was mor
On 6/12/15 8:37 AM, Albert wrote:
Hello:
I am just wondering is it possible to superimpose the protein backbone in each
frame? I try to do this by command:
trjconv -f md.xtc -s md.tpr -pbc res -center
when it pop up options for center, I select "backbone". However, when I
visualize it in VMD
trjconv -fit rot+trans
T.
On Fri, Jun 12, 2015 at 2:37 PM, Albert wrote:
> Hello:
>
> I am just wondering is it possible to superimpose the protein backbone in
> each frame? I try to do this by command:
>
> trjconv -f md.xtc -s md.tpr -pbc res -center
>
> when it pop up options for center, I se
Hello:
I am just wondering is it possible to superimpose the protein backbone
in each frame? I try to do this by command:
trjconv -f md.xtc -s md.tpr -pbc res -center
when it pop up options for center, I select "backbone". However, when I
visualize it in VMD, the protein in trjaceotry is not
Hi,
Top need not be indicative. Run the same with -nt 1 and observe whether the
performance changes. And don't run anything else on these cores.
Mark
On Fri, 12 Jun 2015 14:20 Jan Jirsák wrote:
> Hi,
>
> I have one more problem with running this system with thread-MPI
> (tested in both 5.0.4 a
Hi,
I have one more problem with running this system with thread-MPI
(tested in both 5.0.4 and 5.0.5 on two different machines). When I set
everything as you advised me, it runs, however top command shows only
100% load - i.e., only single CPU is used (and it is really very very
slow), despite log
Thank you Michael!
Best regards
On Fri, Jun 12, 2015 at 1:19 PM, Michael Shirts wrote:
> The 'compressibility' in the pressure coupling is not actually the
> compressibility of the fluid; it's another way to write the mass of the
> fictitious piston. It affects the inertia of the piston and
The 'compressibility' in the pressure coupling is not actually the
compressibility of the fluid; it's another way to write the mass of the
fictitious piston. It affects the inertia of the piston and the period of
the oscillations of the box, but won't affect the magnitude of fluctuations
of the bo
Best regards
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Hi,
I simulate a molecule in NPT ensemble, which I can not find any
experimental data about it's compressibility, what should I put in .mdp
file for it's compressibility in pressure coupling?
Best regards
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Dear GROMACS users:
Does anybody uses gromacs (actually 4.6.7) compiled with MinGW
on windows PC?
I'd been using that without any troubles.
However, quite recently, I firstly tried pdb2gmx (gromacs-4.6.7 compiled
with MinGW on windows PC) and met the trouble.
(I'm not bio-related person and I did
Hi,
do I interpret table 5.5 (Gromacs 4.6.7) correctly that function type 2
in section [pairs] can be used to realize mixed 1-4 scaling as it is
necessary with mixing e.g. an AMBER protein force field with the GLYCAM
force field? GLYCAM doesn't scale 1-4 interactions.
Thanks,
Hannes.
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