Hello Mirzaei
Total how many columns are present in the xvg file?
Paste your data here, then we will know how to plot that.
Thanks
Hi,
I've run a fairly long (1 microsecond) trajectory of ubiquitin in spc/e
on a supercomputer that allows a 48-hour runtime on their nodes. Since
the simulation doesn't finish in 48 hours, I used the checkpoint files
from the simulation to restart the simulation, using the following mdrun
Hi,
Sorry, that's not great wording on our part, I'll fix it. As Eiso said,
only simulations using the [ intermolecular_interactions ] are affected
Mark
On Tue., 18 Jun. 2019, 16:44 Eiso AB, wrote:
> Hi Mateusz,
>
> The intermolecular interactions meant here are the one that can be
>
Hi Mateusz,
The intermolecular interactions meant here are the one that can be
specifically defined as
[ intermolecular_interactions ] in the topology (e.g. used to define
distance restraints, between different molecules, see the manual).
So you shouldn't have to worry about the general
Dear list,
This has been discussed many times previously on the list, but I still have
some questions about hydrogen bond autocorrelation functions.
I have run a simulation with single molecule of a compound in water which
can form exactly one inter-molecular hydrogen bond. From the hbnum.xvg
try
"xmgrace 'filename.xvg'" instead
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Mahmoud
Mirzaei
Sent: Tuesday, June 18, 2019 6:31:25 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] XVG Plotting by Grace
Dear GMX
Dear GMX Users,
in Gromacs 18.1, May you please kindly help me with this command:
When I am trying to plot xvg by grace, I only see such thing...
nanolab@nanolab:~/gx01$ grace pressure.xvg
grace:1>
grace:2>
grace:3>
grace:4>
grace:5>
grace:6>
grace:7>
grace:8>
grace:9>
grace:10>
Many thanks.
Great! Thanks!!!
-Israel
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Dallas Warren
Sent: Monday, June 17, 2019 10:31:43 PM
To: GROMACS users
Subject: Re: [gmx-users] Grompp not producing tpr files
Before you go any further you need to
Dear Developers,
I have read your latest release and I cannot work out how it affected my
simulations. The overall description is very general and implies that all
simulations done with 2019.0-2 should be discarded. If I
understand correctly, most of the simulations run nowadays use domain
Hello gromacs users,
For MD simulations of a peptide in vacuum, I want to find OPLS force field
compatible parameters for modified alanine residue in the peptide (with the
carbonyl oxygen protonated .i.e. enol tautomer of peptide bond). Such a
protonation site is possible in gas phase.
I was
Hi,
The list can't accept attachments, so if you need to share a file, please
use a file sharing service and share the link. However, the usual approach
here is to use "flat-bottomed position restraints"
Mark
On Tue, 18 Jun 2019 at 12:45, ehsan shahini wrote:
> Dear all,
>
> For the study of
Dear all,
For the study of adsorption properties of a small molecule on a substrate
(such as graphene), I would like to constrain the spatial mobility of the
small molecule into a small cylindrical (or cubic) region so it can only
move inside the region. A schematic image of my problem is
Hi,
You're using quite an old version of GROMACS, which unfortunately means the
warning message issued by GROMACS 2018 and more recent is not available to
you (
Hi!
I am trying to run a simulation of a membrane protein (without the
membrane), and to this end I am trying to fix the region of the protein
that is inserted in the hydrophobic part of the membrane. It is not a
transmembrane protein, just an helix is"touching" the lipophylic part of
the
Dear all,Given that I'm using UFF for all atoms in MOF,Is it true that I build
a water molecule from "http://software-lisc.fbk.eu/obgmx/index.php; site and
include it on my topol.top??
Thanks,Ganj
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