Dear collegues!
Oppositely to the Bipin Singh's question I wounder to know about the
exploring ( radius expansion) mode of EDS. For example I define
essential
subspace from some collective coordinates and then run MD in that
subspace in exploring mode of EDS. Will the system be biased to the
some
Hi Bipin Singh,
the parameters -deltaF0, -deltaF, -tau, -alpha, and -T are used only
for flooding and have no effect in pure essential dynamics. Which coordinates
appear in the output trajectory (*.trr, *.xtc) is exclusively controlled
by .mdp options (i.e. the group you select there), not by the
Dear Sir,
Thank you Sir for the clarification.
Need to explore about this.
Thanking you
With Regards
M. Kavyashree
On Wed, Jun 8, 2011 at 2:35 PM, Tsjerk Wassenaar wrote:
> Hi Kavya,
>
> > Thanks sir. I will go through them. However I have referred -
> > "A Tutorial on Principle component
Hi Kavya,
> Thanks sir. I will go through them. However I have referred -
> "A Tutorial on Principle component Analysis" by Lindsay I Smith.
> Which gave a good understanding about the concepts. Still I
> have some doubts regarding eigen values, as you have told
> I will think over them again.
I
Dear Sir,
Thanks sir. I will go through them. However I have referred -
"A Tutorial on Principle component Analysis" by Lindsay I Smith.
Which gave a good understanding about the concepts. Still I
have some doubts regarding eigen values, as you have told
I will think over them again.
But one sta
Hi Kavya,
> Its g_covar contributed by Dr. Rossen apostolov if I am right. Here it
> states that those which are having correlation coefficient better than 0.5
> will be reported, so covariance gives those which have correlation
> coefficient
> less than 0.5?
I don't know the modified version. B
Dear Sir,
Thanks for giving a clearer picture about essential dynamics. I was very
eagerly awaiting for a reply. Thanks you very much :).
No, ED does not make any assumptions on the nature of motions. It does
> not distinguish anharmonic from harmonic motions. It also does not
> distinguish
Hi Kavya,
On Sat, Jun 4, 2011 at 8:18 AM, Kavyashree M wrote:
> Dear Gromacs users,
>
> I am new to essential dynamics, I have gone through
> some fundamentals in PCS, the mailing list related to ED
> and few publications by -
> Amadei (Proteins, 17, 412-425, 1993),
> a. Amadei (journal of biomo
- Original Message -
From: pawan raghav
Date: Tuesday, August 17, 2010 20:14
Subject: [gmx-users] Essential Dynamics
To: gmx-users@gromacs.org
> Dear Tsjerk, > > It will be helpful to me if you would like to solve my
> problem I have already read your tutorial and so many papers but I
Hi Pawan,
This goes beyond a few lines of explanation. Move away from the tools
g_covar and g_anaeig slowly ;) and do some more background reading on
principal component analysis. I've tried to explain it in my tutorial
at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html (which
will prob
On 05/20/2010 10:40 AM, Carla Jamous wrote:
Hi everyone,
Please I need a piece of information not related to gromacs.
I'm searching for a document or article that may explain Essential
Dynamics to beginners.
Thanks
Carla
and of course, in a more practical way:
http://www.gromacs.org/Docume
On 05/20/2010 10:40 AM, Carla Jamous wrote:
Hi everyone,
Please I need a piece of information not related to gromacs.
I'm searching for a document or article that may explain Essential
Dynamics to beginners.
Thanks
Carla
http://www.ncbi.nlm.nih.gov/pubmed/8108382
AKA "how the molecular dyna
Hi Chris,
the segfault was due to the fact that with the sd integrator the constraints
have to be evaluated twice and in the second call there is no pointer to
the velocities present. I have fixed that in the master and release-4-0-
patches branches. The velocity correction is now only done when v
Hi JJ,
> 1) Should ED analysis be performed only on the segment of trajectory wherein
> the protein's RMSD has equilibrated, am I right? Because I have the notion
> that harmonic analysis of a trajectory can only be performed when the
> protein is undergoing fluctuations about a minimum. In other
Euston, Stephen R wrote:
> Hi,
>
>
>
> I am hoping to use essential dynamics to look at unfolding of proteins
> (probably barley lipid transfer protein and bovine beta-lactoglobulin).
> I have searched the Gromacs database, and the web but I can find very
> little info on the actual process of
I've rerun everything from scratch following Bert's input. The numbers
seemed all right, but the runs still failed. Then I tried using just a
subset of the eigenvectors, which has worked so far (i.e. it's running
for about 1ns).
Bert and Lars - thanks a lot for your help,
Ran.
Bert de Groot wrote
Ran Friedman wrote:
Dear Bert,
The Jacobi error hints at a fitting problem. If not the starting
position, could it
be the target that's causing the problems?
Please check the head of the .edo and log files, to see if the
reported RMSD's
are what you would expect and especially if reported proj
Dear Bert,
>
> The Jacobi error hints at a fitting problem. If not the starting
> position, could it
> be the target that's causing the problems?
>
> Please check the head of the .edo and log files, to see if the
> reported RMSD's
> are what you would expect and especially if reported projections a
Ran Friedman wrote:
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
The Jacobi error hints at a fitting problem. If not the starting position,
could it
be the target that's causing the problems?
Please check
Hi Ran,
ok, that's strange. did you try to run it in double prec?
Lars
Ran Friedman wrote:
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
Large VCM(group rest): nan, nan, nan,
ekin-c
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
Large VCM(group rest): nan, nan, nan,
ekin-cm: nan
In the log file.
Ran.
Lars Schaefer wrote:
> Dear Ran,
> this could mean that
Dear Ran,
this could mean that you have problems fitting to your reference structure.
Lars
Ran Friedman wrote:
Dear all,
I'm resending this message (please see below) with some additional
info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -d
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