Hi all,
Just a quick question - and perhaps some wisdom from those with more experience.
I am trying to use metadynamics with gromacs to plot an energy landscape about
the rotation of two proteins. If I were to define my collective variables as
ThetaA and ThetaB, Theta being the rotation about
Hi all,
I would imagine this has been covered before, yet I don't think I have
unearthed the right search inquiry yet.
I want to make a dihedral angle along the length of a helical protein using the
vectors (A, B, C), (B, C, D), where B is a C-alpha on the helix backbone, and A
, C and D are
Apologies if this has been covered once before, I've had a hearty search and
I've yet to find anything.
I have just installed a modified verison of Gromacs 4.0.2 which calculate
lateral pressure. However, when I run grommp I get:
Residue numbers in the .top are not numbered consecutively from
:17
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] renumbering residue numbers for version 4.0.2
On Fri, Mar 29, 2013 at 2:10 PM, Nash, Anthony
anthony.n...@warwick.ac.ukwrote:
Apologies if this has been covered once before, I've had a hearty search
and I've yet to find anything
in that prehistoric era... Without seeing what
numbers things have, it's hard to say anything useful.
Mark
On Fri, Mar 29, 2013 at 6:26 PM, Nash, Anthony
anthony.n...@warwick.ac.ukwrote:
Thanks for that, I've renumbered the residues in the .gro file, and even
so far as in the respective protein .itp
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_wham missing option
On 2/2/13 12:58 PM, Nash, Anthony wrote:
Hi All,
I am using Gromacs 4.5.5 and running free energy calculations. According to
the article g_wham - A Free Weighted Histogram.. (J. Chem. Theory.
Comput. 2010, 6
Hi All,
I am using Gromacs 4.5.5 and running free energy calculations. According to the
article g_wham - A Free Weighted Histogram.. (J. Chem. Theory. Comput.
2010, 6, 3713-3720), there is the option -bs-method. However, I am unable to
find this option when running g_wham. I want to use
Dear gmx users,
I posted a couple of weeks ago with regards to correctly using umbrella
sampling and the WHAM on atomistic transmembrane proteins with a reaction
coordinate as a function of interhelical distance. I have a single TM dimer,
but with a different transmembrane domain face at the
Transmembrane proteins
On 12/30/12 12:28 PM, Nash, Anthony wrote:
Dear gmx users,
I posted a couple of weeks ago with regards to correctly using umbrella
sampling and the WHAM on atomistic transmembrane proteins with a reaction
coordinate as a function of interhelical distance. I have a single TM
...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 December 2012 20:08
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PMF Transmembrane proteins
On 12/30/12 2:57 PM, Nash, Anthony wrote:
Dear Justin
Thanks for your reply.
I am studying a TM peptide, looking at how
Good morning,
A bit of a long one I am afraid.
I am simulating a transmembrane dimer, and calculating the association free
energy through potential of mean force calculations as a function of
interhelical distance. I have got very good umbrella coverage along my reaction
coordinate, however,
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 19 December 2012 13:23
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Where to stop with TM protein PMF calculations
On 12/19/12 4:12 AM, Nash, Anthony wrote
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