Hello Hind,
There HREMD is available for Gromacs patched with PLUMED, and there is a
tutorial you can go through:
https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html
All the best,
Qinghua
On 1/18/20 8:12 PM, hind ahmed wrote:
Dear,
is there a tutorial to run Hamiltonian replica exchange
Dear,
is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could
you please see if the mdp setting is right to run Hamiltonian replica exchange
of lipid system using a coarse-grained method?
integrator = sd
tinit= 0.0
dt
Hi,
You certainly want the code to take the path where lambda varies, but if
you comment out the check for unequal lambda and avoid the check that T is
unequal, things should work fine.
Mark
On Thu, Mar 8, 2018 at 2:59 AM Carlo Martinotti <
carlo.martino...@postgrad.curtin.edu.au> wrote:
> Hell
Hello everybody,
So i am trying to set up a replica exchange with solute tempering simulation
for my membrane-drug systems. We modified the gromacs source code in a way that
allows the modification of the hamiltonian of singular pairs of interactions
(eg solute-water, solute-solute, ion-solute
asons that this REST fork of plumed was
created in the first place.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of 呂宗諭
Sent: 13 May 2015 11:29
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Hamiltonian r
Dear all,
I would appreciate you to give me any comments or share your experience on
the question below.
I am trying to run Hamiltonian replica exchange with solute tempering
(H-REST) in either 5.02 or 5.04 version to speed up the conformation
sampling of my protein along with a caging small mole
Hi,
I have come to understand that this might be doable with the newest gromacs
versions 5.x (and without plumed).
Can someone verify this? And if yes would he/she be so kind as to provide a
sample .mdp file demonstrating how the pull code and the free energy code
are communicating to succeed thi
On Fri, Jun 27, 2014 at 11:36 AM, Thomas Evangelidis wrote:
> Thank you all for your comment!
>
> The helix dimer is not very stable and I know that from extensive
> accelerated MD simulations I've done with AMBER using various boost values.
> Now I want to use a different force field available on
Thank you all for your comment!
The helix dimer is not very stable and I know that from extensive
accelerated MD simulations I've done with AMBER using various boost values.
Now I want to use a different force field available only in GROMACS, and
though partial solute tempering HREX as the most su
PS: [Perhaps stating the obvious] Using an overly aggressive
Hamiltonian scaling will only result in bad mixing at high
temperatures and therefore low efficiency, hence wasted compute time,
but it should not "hurt" your results. It is still quite useful to
ensure that you're not sampling an entire
Hi,
Next time, you should perhaps use "plz, ..." (and other eye-catching
formatting marks); a nice mix of font colors and typefaces could also
help to highlight your questions. :D
On Tue, Jun 24, 2014 at 10:32 PM, Thomas Evangelidis wrote:
> Greetings,
>
> I want to use the HREX implementation o
Indeed. REST implemented in PLUMED seems a good bet.
Mark
On Jun 24, 2014 11:50 PM, "HANNIBAL LECTER"
wrote:
> I would think of using Replica Exchange with Solute Tempering in this case.
> Look at the paper as to how one can implement this in Gromacs (doi:
> 10.1002/jcc.21703).
>
> Without havin
I would think of using Replica Exchange with Solute Tempering in this case.
Look at the paper as to how one can implement this in Gromacs (doi:
10.1002/jcc.21703).
Without having more details I would suggest to you to scale the Hamiltonian
of each replica such that the Helix bundles are always cor
Greetings,
I want to use the HREX implementation of GROMACS to study the dynamics of a
heterodimeric protein. The structure is a two helix bundle (two helical
monomers that are wrapped around each other) with disordered ends. I am
mainly interested in the dynamics of the disordered ends because I
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