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 f
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
wrote:
> Thanks for that, I've renumbered the residues in the .gro file, and even
> so far as in the respective protein .itp file
gromacs.org] on behalf
of Mark Abraham [mark.j.abra...@gmail.com]
Sent: 29 March 2013 14:17
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
wrote:
> Apologies if this has been covered onc
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
: 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. C
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 b
...@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 p
ct: Re: [gmx-users] PMF 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
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 he
thanks
Anthony
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
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,
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