Den 2020-02-12 kl. 23:07, skrev Live King:
Dear all,
I am running a simple test case with a lipid bilayer (DMPC), water, and
ions (150mM KCL) under the influence of a constant electric field ( 300mV,
500mV, and 700mV). *I expected positive and negative ions to separate in
the presence of an
Den 2020-02-13 kl. 05:10, skrev Pathum Manjula Weerawarna:
Hi everyone,
I'm trying to estimate the configurational entropy of a small molecule using
gmx anaeig. However, it does not allow me to use a mass-weighted covariance
matrix for the calculation (only allow me to use mass-unweighted CV
Hi everyone,
I'm trying to estimate the configurational entropy of a small molecule using
gmx anaeig. However, it does not allow me to use a mass-weighted covariance
matrix for the calculation (only allow me to use mass-unweighted CV matrix).
Theoretically, the use of a mass unweighted CV
Dear all,
I am running a simple test case with a lipid bilayer (DMPC), water, and
ions (150mM KCL) under the influence of a constant electric field ( 300mV,
500mV, and 700mV). *I expected positive and negative ions to separate in
the presence of an external electric field*. However, I am not
Dear Gromacs users,
I’ve got a question regarding the tabulated potentials for bonded interactions.
Gromacs recognises and reads the non-bonded potential tables through the energy
groups specified. But how can I refer each bond type to its table?
I have derived coarse-grained potentials for a
Dear Gromacs Users,
I'm now simulating a water droplet with some vacuum space in a NVT
ensemble. I'd like to calculate the excess free energy for different shells
of the droplet via test particle insertion method, which I assume I should
first calculate the COM of the droplet, and then divide the
Paul,
thank you very much!
Cheers,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Paul Bauer
Sent: 12 February 2020 21:02
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] generating Doxygen documentation
The correct
The correct address is
http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml
Need to fix a link somewhere then I think.
/Paul
On Wed, 12 Feb 2020, 20:46 Michele Pellegrino, wrote:
> Moreover: the link to Jenkins does not work (section 7.8.1,
Moreover: the link to Jenkins does not work (section 7.8.1, "Building the
documentation"):
http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml
Cheers,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
Mark,
no such directory is produced after make (evein if the output is 'Built target
doxygen-all').
The only Doxyfile I can utilize to generate html/latex documentation is
'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'.
It seems I need to run cmake somewhere, somehow, but
Sounds good. Thanks.
On Wed, Feb 12, 2020 at 1:22 PM Paul bauer wrote:
> Hello,
>
> please do ***NOT*** use the mailing list for those kinds of
> announcements in the future.
> It is supposed to be for people discussing and asking for help with
> GROMACS, not for advertising conferences.
>
>
I'm using
Ubuntu 18.04.3 LTS
On Wed, Feb 12, 2020 at 7:52 PM Benson Muite
wrote:
>
> Hi,
> What platform are you building on? Last time I tried this, there were a
> few extra dependencies I needed to install.
> Benson
>
> On Thu, Feb 13, 2020, at 12:34 AM, Mark Abraham wrote:
> > Hi,
> >
> >
Hi,
What platform are you building on? Last time I tried this, there were a few
extra dependencies I needed to install.
Benson
On Thu, Feb 13, 2020, at 12:34 AM, Mark Abraham wrote:
> Hi,
>
> When they succeed, the doxygen targets produce files like
>
>
Dear gmx comunity,
I am trying to use gmx analyze for the block analysis and I get this error:
Fatal error:
This build of GROMACS was not configured with support for lmfit, so the
requested fitting cannot be performed. See the install guide for
instructions
on how to build GROMACS with lmfit
Hi Marko,
I apologize for the slow response.
"pdb2gmx" is not an executable, but an argument. Try
gmx.commandline_operation(
'gmx',
['pdb2gmx', '-water', 'spce', '-ff', 'oplsaa']
...)
I hope to be able to improve the documentation soon, but the exception
should have
Hello,
please do ***NOT*** use the mailing list for those kinds of
announcements in the future.
It is supposed to be for people discussing and asking for help with
GROMACS, not for advertising conferences.
Thanks
Paul
On 12/02/2020 19:13, Jihong Ma wrote:
Dear colleagues,
The Society of
Dear colleagues,
The Society of Engineering Science (SES) 57th Annual Technical Meeting will
be held at Hyatt Regency Minneapolis, September 28-30, 2020 (
https://ccaps.umn.edu/SES).
As part of this meeting, we are organizing a mini-symposium addressing
the *advances
in polymer modeling and
Hi,
When they succeed, the doxygen targets produce files like
$builddir/docs/html/doxygen/html-*/index.xhtml
which you can open in your browser. The doxygen for the released versions
is on the web however, so it's much easier to just use or refer to that.
Mark
On Wed, 12 Feb 2020 at 16:30,
Hi,
I am trying to generate the Doxygen documentation for GROMACS from the files in
/docs/doxygen.
I following 2020 manual, I run 'make doxygen-all' in the build directory,
succesfully; I don't know what to do next: I tried to run cmake in the doxygen
directory to generate the Doxyfiles, but
On 2/12/20 6:20 AM, Gonzalez Fernandez, Cristina wrote:
Dear Gromacs users,
I'm trying to perform a protein-lipid complex simulation. While the interaction
between these molecules seems reasonable, the protein Root Mean Square
Deviation is too high, and I don't know how to stabilice it.
On 2/12/20 8:23 AM, Peter Mawanga wrote:
Thanks a lot sir for your reply.
Since experiments take place over hours but the simulations can at best
approach millisecond levels. I was wondering if there is an acceptable time
conversion factor from experiments to simulations. For example, the
On 2/11/20 4:46 PM, sai manohar wrote:
You cannot generate the desired parameters (.itp) for metals in the ATB
server. In fact even CGenFF or RED server are also not useful for metals.
However, if you have access to any DFT modeling in house to perform QM
calculations using Gaussian etc., you
Thanks a lot sir for your reply.
Since experiments take place over hours but the simulations can at best
approach millisecond levels. I was wondering if there is an acceptable time
conversion factor from experiments to simulations. For example, the
simulation data generated over a 350 ns period
> Dear group members
>
> My sincere apologies for the non-Gromacs related question, but I require
> this information urgently and hence posted my query here.
>
> Could someone please provide me with any guidelines to appropriately model
> experimental processes with molecular dynamics simulations?
Dear Gromacs users,
I'm trying to perform a protein-lipid complex simulation. While the interaction
between these molecules seems reasonable, the protein Root Mean Square
Deviation is too high, and I don't know how to stabilice it. Could you
recommend me any simulation trick to stabilize the
Dear group members
My sincere apologies for the non-Gromacs related question, but I require
this information urgently and hence posted my query here.
Could someone please provide me with any guidelines to appropriately model
experimental processes with molecular dynamics simulations?
Since the
Hi,
On Wed, Feb 12, 2020 at 8:54 AM TIASHA ADHIKARY wrote:
> Hello,
> I am trying to calculate FEP using gromacs. I have used pmx for initial
> structure and .itp file.
> I am getting the following warning
>
> WARNING 1 [file MOL.itp, line 185]:
> Some parameters for bonded interaction
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