If the GROMOS force-field would clearly not be compatible with GROMACS, we
would have removed it from the GROMACS distribution.
There are two issues here, which both stem from the fact that the GROMOS
force-field has been parametrized with a simulation setup that, for good
reasons, can not be
?
By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers (if
that may help understanding the issue).
Thanks,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Berk Hess
Sent: 22 January 2020 16:49
To: gmx-us
How are you counting the elements? Lines with 3531 elements are very long, so
they can easily exceed some limit.
/Berk
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Michele
Pellegrino
Sent: Tuesday, January 21, 2020 5:16 PM
To:
Hi,
Using center of mass motion removal in combination with an absolute reference
in the system, such as position restraints, will always lead to artifacts, as
physical motion is removed and not drift due to numerical rounding errors. For
the most common case of equilibrating macromolecules
Hi,
You should not use direction-periodic, you don't want to pull more than half
the box size, I presume.
Your pull rate is extremely high 50 nm/ns. I would start by lowering this.
Cheers,
Berk
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on
are FF development and
finding bugs in my FF. Although the absolute energies are meaningless it
would be nice if they could be intuitively correct.
Best regards and thanks again!
Sergio
On Fri, Mar 29, 2019 at 1:45 PM Berk Hess wrote:
> Hi,
>
> The negative energy is due to th
Hi,
The negative energy is due to the uniform background charge that appears when
your system has a net charge, not due to shifting of pair interactions.
Computing the absolute energy of a periodic system with net charge is
meaningless.
Cheers,
Berk
From:
Hi,
Indeed, the former can be very beneficial, even in the case all replicas start
at the same point.
The latter is an interesting idea (even better when using REST instead of
T-REMD), but would require adaption of the exchange criterion. Just exchanging
ignoring the bias will likely give
gmx energy -b -e -odh should extract the xvg file you want from the energy file.
Berk
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Qasim Pars
Sent: Friday, March 1, 2019 8:38 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] edit
Yes, this is due to an improvement.
Set the pbcatom (as the error message tries to say) for the pull groups
mentioned. The options are described in the mdp section of the manual.
Berk
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Mark
I will now further adjust the parameters based on what you said. Also
with the 2D bias, gmx awh now generates a 2D PMF as a XYZ triplet which
I can plot easily, so thanks also for that.
Cedric
Le 2/15/2019 à 3:50 PM, Berk Hess a écrit :
> Your initial error parameters is orders of magnitude
-r--r--. 1 cleyrat granier 7.5G Feb 14 20:51 step7_awh5_step96200.cpt
-bash-4.2$
Is this some kind of bug or am I doing something wrong with the parameters?
Cedric
Le 2/14/2019 à 8:09 PM, Berk Hess a écrit :
> Note though, as also noted in the manual, you need to be careful what you
>
-bash-4.2$
Is this some kind of bug or am I doing something wrong with the parameters?
Cedric
Le 2/14/2019 à 8:09 PM, Berk Hess a écrit :
> Note though, as also noted in the manual, you need to be careful what you
> wish for. 2D biasing leads to uniform sampling of the requested recta
on the free-energy.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Berk Hess
Sent: Thursday, February 14, 2019 5:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] AWH with two bias potentials
I see now that you used awh-nbias=2 with awh-ndim
reaction
coordinate from gmx awh. Each file has two columns (x=coordinate 1,
y=PMF or x=coordinate 2, y=PMF). My coding and maths skills are quite
limited so if you have a script that can convert these data to a 2D
format, I would be happy to use it.
Cedric
Le 2/14/2019 à 3:27 PM, Berk Hess a écrit
gmx awh writes out the 2D (or any-D) PMF to xvg files for different times. The
1D nature of xvg files is not convenient for visualization though, so you need
to write a script to convert it to you favorite 2D data format. I probably have
a script somewhere for some 2D format (python?) if you
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