Dear All,
Thanks for the reply. Then is any single trjconv command available before
viewing the trajectory file, or before extracting the xtc file, with that
command all the fraud caused by the PBC effect will be got rid of?
In addition, the box in the e-mail of Dr Dallas Warren should be the
On 14/08/2012 5:54 PM, Acoot Brett wrote:
Dear All,
Thanks for the reply. Then is any single trjconv command available before
viewing the trajectory file, or before extracting the xtc file, with that
command all the fraud caused by the PBC effect will be got rid of?
I linked a page with a
You are missing a major conceptual principle of MD here.
See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Read manual, section 3.2
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal
From your comments, it appears that you have not watched the trajectory for
you system. This is really something that everyone should do with the systems
they are simulating, as you can gain a lot of information from looking
visually at it. Looking at 0.5ns snap shots is not watching the
On 14/08/2012 7:53 AM, Dallas Warren wrote:
From your comments, it appears that you have not watched the trajectory for
you system. This is really something that everyone should do with the systems
they are simulating, as you can gain a lot of information from looking visually at
it.
Dear Albert,
I hope I can support my MD results with some bioinformatics data. For
example, it indicates the highly movavle residue I mentioned in my previous
e-mail is not conserved at all, and it is only specific that structure.
For your 10X with different seed simulation, does it mean the
On 8/11/12 7:25 PM, Acoot Brett wrote:
Dear Albert,
I hope I can support my MD results with some bioinformatics data. For
example, it indicates the highly movavle residue I mentioned in my previous
e-mail is not conserved at all, and it is only specific that structure.
For your 10X with
On 8/11/12 7:49 PM, Acoot Brett wrote:
Dear Justine,
For aideal protein system (no local minima in the MD), regardless of what the
seed number is, the system will converge to a same conformation, rihgt?
Not really - a single structure tells you nothing. Individual simulations
should
Dear Dr. Dallas Warren,
My protein is a protein-peptide complex. The residues I mentioned which moves
in a large scope is from the peptide, it is the last 3rd residue of the
peptide, a lysine.
I compared this lysine position with the other residue positions (including the
peptide binding
On 8/10/12 7:58 PM, Acoot Brett wrote:
Dear Dr. Dallas Warren,
My protein is a protein-peptide complex. The residues I mentioned which moves
in a large scope is from the peptide, it is the last 3rd residue of the
peptide, a lysine.
I compared this lysine position with the other residue
Dear Justin,
Can you explain to me what do you mean for trjconv -pbc mol -ur compact
followed by trjconv -center. Does it mean 2 steps command, with the first step
as trjconv -pbc mol -ur compact and the second step as trjconv -center? Or
can we merge it as a single step step?
Second, will
On 8/10/12 8:19 PM, Acoot Brett wrote:
Dear Justin,
Can you explain to me what do you mean for trjconv -pbc mol -ur compact followed by trjconv
-center. Does it mean 2 steps command, with the first step as trjconv -pbc mol -ur compact
and the second step as trjconv -center? Or can we merge
you have to submit 10X with different seed simulation to confirm your
results. 10ns is not converged for some simulation, you should also
extend it in nowadays timescale level.
Moreover, if you don't have biochemistry data to support your idea,
nobody will believe your results.
good luck
Dear Catch ya,
I have watched the trajectory of the simulation. Besdies, I got the PDb file
for the whole 10 ns MD every 500 ps. Then I compared all the PDB files
generated, and it confirms that 1 specific residues moves in an extremely large
space.
Can you give me an explaination on it?
That's hard to judge for everyone but you, because there are too many questions
left. What kind of residue is it? Is it at one of the protein termini, is it on
the surface or buried by other sections? Are there interactions with other
parts of the system? Did you check the RMSD or RMSF-values
No, I can't, since you are the one with all the information in front of you,
and I only have a couple of sentences filtered through you on what is going on.
Some questions you can ask yourself to help answer the question you have:
And what did the residue do while you watched the
Dear Marck,
Will you please give me some suggestions on how to decide whether the probelm
is from periodic boundary conditions?
Cheers,
Acoot
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent:
What information has told you that you have large scale movement? Where did
that information come from, how was it generated? Have you watch the
trajectory of this simulation to see how the residue actually moves?
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of
Dear All,
I have a protein with about 400 amino acids. I have done a production MD of it.
I find in the 400 amino acids, there is 1 amino acids, during the whole MD
process, this residue moves in a extremely large scope in comparison with all
the other residues.
Do you think this single
On 6/08/2012 8:58 PM, Acoot Brett wrote:
Dear All,
I have a protein with about 400 amino acids. I have done a production MD of it.
I find in the 400 amino acids, there is 1 amino acids, during the whole MD
process, this residue moves in a extremely large scope in comparison with all
the
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