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
Hello All,
I want to use the essential dynamics (ED) sampling method to simulate the
unfolding to folding process using make_edi option of GROMACS. For this
task I am using -radcon option (acceptance radius contraction along the
first two eigenvectors towards the folded structure (b4md.gro)) of m
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
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 biomolecular structure and dynamics, 13, 615, 1996)
b. Berk Hess (Physical reviews
Hi,
I am running essential dynamics for a protein in water system (charmm-nocmap
and tip3p). I use the first 25 eigenvectors and targeted ED. It stops after
630ps when settle and lincs start giving warnings.
Step 315573, time 631.146 (ps) LINCS WARNING
relative constraint deviation after LINCS:
- 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
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 am really confused and
thats why mail to you. So please answer me which will help me lot to
understand right concept.
--
Pawan
--
gmx-users mailing listgmx-
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
Hi all,
I have a confusion regarding "Essential Dynamics". I have read so many
papers regarding PCA and ED most of the papers among them explained
eigenvectors and eigenvalues are as follows:
if a protein has 207 C alpha residues then the total no of eigenvectors are
3N X 3N, where N= no. of atom
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 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
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search th
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
Hello,
In my hands, mdrun throws a segfault when passing the -ei flag to
mdrun and utilizing the sd integrator. I'll admit that I have only
tried this with a single system. Nevertheless, using -linacc vs.
-linfix makes no difference, neither does moving to constraints=none
or parallel vs.
Hi everyone,
I am very new to essential dynamics analysis, and trying to determine the
similarity/dissimilarity between two different MD trajectories.
I projected the eigenvectors of trajectory-2 unto the first-two eigenvectors of
trajectory-1 using g_anaeig with the -2d option and generated a p
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
Hi!
I have a 7ns MD run of a protein and the RMSD of the protein had stabilized
after 3ns.
I am about to performed essential dynamics (ED) analysis (using the commands
g_covar and g_anaeig) on the trajectory and I have a few
questions/clarifications.
1) Should ED analysis be performed only on th
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
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 running the simulation. I have also
looke
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
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 -debug flag and got some "nan" values in
mdrun.log:
dekin = nan, ekin = 175815 vcm = ( nan nan nan)
m
Dear all,
I'm trying to run MD with ED sampling. The target structure is a protein
taken from one simulation, the .tpr file is taken from a different one.
I'm using a subset of the CA atoms to calculate the eigenvectors. The
problem is that the MD run crashes after set-up.
Depending on the machin
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