> Dear experts,
> I have done upto minimization but faults in equilibration I am again
> starting the minimization, now in adding ions of sodium the following
> error is given, what is the reason for this.
> Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
> Warning: atom names i
Dear experts,
I have done upto minimization but faults in equilibration I am again starting
the minimization, now in adding ions of sodium the following error is given,
what is the reason for this.
Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
Warning: atom names in topol.to
Hello,
I need to be able to remove the COM motion of a defined group only in
x-direction and y-direction but not the z-direction. Is there a way to do
this in GROMACS? The comm_mode options removes ALL components of the COM
motion of the defined group.
Thank you.
_
Evanildo Júnior wrote:
Dear gmx-users,
I would like to minimize the potential energy of the active site of an
enzyme. Because I do not have too much computer power to perform a full
enzyme calculation, I need to create three different zones in which the
calculation will take place. The first
SWAPNA wrote:
> Dear gmx users,
> I am using g_anaeig to filter my traj along the first eigenvector.
>
> 'g_anaeig -b 5000 -f 15000 -v eigenvec.trr -f calpha.tpr -s calpha.xtc
> -first 1 -last 1 -filt alongeigvec1 -dt 100'
> 5000ps to 15000ps has equilibriated trajectory. So I am using that to
>
Hi all,
searching in the ml I found this thread:
http://www.gromacs.org/pipermail/gmx-users/2006-April/021256.html
about comm-mode=angular and the method described in
J. Chem. Phys. 112(1) pp. 9-23 to remove com translation and rotation.
I was not able to download the modified versions of the co
Dear gmx-users,
I would like to minimize the potential energy of the active site of an enzyme.
Because I do not have too much computer power to perform a full enzyme
calculation, I need to create three different zones in which the calculation
will take place. The first one is the outer boun
rs mailing listgmx-users@gromacs.org
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> Can't
Dear gmx users,
I am using g_anaeig to filter my traj along the first eigenvector.
'g_anaeig -b 5000 -f 15000 -v eigenvec.trr -f calpha.tpr -s
calpha.xtc-first 1 -last 1 -filt alongeigvec1 -dt 100'
5000ps to 15000ps has equilibriated trajectory. So I am using that to
perform essential dynamics.
W
Apparently, my documentation for topolbuild is not
sufficiently precise in the definition of the input
molecular structure file.
The program, topolbuild, is described as taking a mol2
file as input. By mol2 file, I mean a syntactically
correct mol2 file with Tripos atom types and charges,
and wit
Thank you Sir
If this was fake or not...Me and my dear colleagues had a good laugh,
anyway...also about the nice comments.
Maybe this inspires: http://www.youtube.com/watch?v=qiSkyEyBczU
"Black hole sun, won't you come"
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical
Hello all,
I am simulating pressure driven flow in a nanochannel. To
introduce a pressure gradient in the system I have put all the liquid
atoms in one group and applied acceleration to it. Also I am
periodically removing the centre of mass motion my nstcomm value. My
doubt is that when
Hi Nihar,
unfortunately I can't help you with thioflavin parameterization and
probably other people here will address you to general links. Our CDs
were built on the base of topologies for smaller sugars already
available in the gromos force field (pasting building blocks). I hope
someone else can
Dear Anna,
Use make_ndx to create any group you find useful.
Ran.
Anna Marabotti wrote:
> Dear gmx-users,
> I would like to create from my trajectory an average structure of my protein
> with its ligand inside.
> With both g_rmsf and g_cluster I am prompted to indicate one group, but
> ligand
Dear Anna,
I think you can use make_ndx to make a new group for your ligand+protein. For
example:
$make_ndx -f filename.gro -o filename.ndx
It will list all of the groups in you filename.gro file. Then select your
protein and ligand and make a new name for the group. Use your filename.ndx
ind
Hi Ángel,
Thanks a lot for coming forward. Regarding CD (\alpha, \beta and \gamma) I
will contact you as soon as possible. For the moment I would like to get
the same for Thioflavin-T. It is a fairly big molecules with I think 39
atoms. Can you tell me how go about (procedure in detail) to get t
Dear gmx-users,
I would like to create from my trajectory an average structure of my protein
with its ligand inside.
With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand
and protein are
separated into different groups, and I'd want to exclude water from this
structure,
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