Hi Berk. Thanks for the response. If I am looking to find the free energy of
binding of the peptide to the globular protein, then I do not know how else to
approach the problem besides using my "brute-force" approach. Do you have any
alternative ideas?
Elio Cino
__
rams rams wrote:
Hi,
I run a regular MD on a peptide with several conformations. I want to
estimate the potential energy of each conformer. When I try using
"g_energy" with the option of "Potential" using the corresponding ".edr"
file, I am getting the average potential energy. But I am thinki
Anna Marabotti wrote:
Dear gmx-users,
after a lot of trial (and errors) I finally got my REMD simulation. The
problem was solved essentially when we avoided indicating the extension of
the .tpr files: i.e.
mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_ -np 16
did not work, whereas
mdr
Dear gmx-users,
after a lot of trial (and errors) I finally got my REMD simulation. The
problem was solved essentially when we avoided indicating the extension of
the .tpr files: i.e.
mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_ -np 16
did not work, whereas
mdrun -s REMD_ -multi 16 -r
rams rams wrote:
Hi,
I run a regular MD on a peptide with several conformations. I want to
estimate the potential energy of each conformer. When I try using
"g_energy" with the option of "Potential" using the corresponding ".edr"
file, I am getting the average potential energy. But I am thin
Hi,
I run a regular MD on a peptide with several conformations. I want to
estimate the potential energy of each conformer. When I try using "g_energy"
with the option of "Potential" using the corresponding ".edr" file, I am
getting the average potential energy. But I am thinking that it is the
aver
On Fri, 18 Sep 2009, Vasilii Artyukhov wrote:
Hi,
Anybody have any real-world comparisons of using MKL vs. FFTW3?
[ http://www.quantumespresso.org/user_guide/node16.html
]http://www.quantumespresso.org/user_guide/node16.html says:
Axel Kohlmeyer suggests the following (April 2008): "(I've) f
Hi Soren,
> Why I am seeing this difference? Is it due to round-off’s after the
> transformation to center the molecule in the box? Or am I using g_rmsdist
> wrongly?
It's a bit weird indeed. You might be right that it's due to round-off
errors. You can try to copy the original gro file and repl
Hi Lin,
You should check the manual, check the literature on cross validation
of MD/NMR, and note that the tutorial you've been following has two
items related to it, namely distance analysis, including NOE back
calculation, and calculation of order parameters.
Hope it helps,
Tsjerk
On Fri, S
Dear GMX-users
I have a question about what happens when editconf is used to "box" a
molecule.
The reason I ask is because, I have used g_rmsdist in order to study how
a very small piece of a structure (100+ atoms) relaxes towards its
native state (given by NMR) after a small perturbation.
Hi,
You seem to be trying to decouple a 9 residue peptide from the rest of the
system.
This "brute-force" approach will only work when you have an enormous amount
of computer power and you will have to tune all your parameters carefully.
You should consider if this approach is feasible.
You cra
I don't know if this is worth all the troube.
Gromacs performance is not very dependent on FFT speed (unless you
choose your parameters badly). FFTW is faster than anything else
on most platforms (often including hardware vendor specific FFT's).
Simply sticking to FFTW will probably never result i
> Date: Fri, 18 Sep 2009 16:24:21 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Can Gromacs produce the data from NMR?
>
> Chih-Ying Lin wrote:
> >
> >
> > HI
> > Can Gromacs produce the data from NMR?
>
> No, if my guess at what "data" you mean
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