On 20/11/2010 4:54 PM, Sunita Patel wrote:
Dear Users,
I calculated RMSD for a trajectory with same reference structure using GROMACS
and VMD. I observed completely difference plots for the same data. Please see
the attached file.
What could be the cause for this disparity?
We can't be
Thank you very much, Mark! The problem was for the type CG2 in .rtp. I
corrected it and the errors disappear.[?]
(I should study more for that non-zero charge, i think.)
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I have had a similar experience, I have not investigated it thoroughly at the
moment, but I get different (identical with specific jumps possibly due to pbc)
plots if I take starting structure as my input pdb file or if my starting
structure is first structure of trajectory.
I think the
With topol.tpr file, am getting identical plot as that of VMD.
Thanks,
Sunita
On Sat, 20 Nov 2010 08:39:17 +, X Rules wrote
I have had a similar experience, I have not investigated it thoroughly at the
moment, but I get different (identical with specific jumps possibly due to
pbc) plots
On Sat, 20 Nov 2010 19:05:35 +1100, Mark Abraham wrote
On 20/11/2010 4:54 PM, Sunita Patel wrote:
Dear Users,
I calculated RMSD for a trajectory with same reference structure using
GROMACS
and VMD. I observed completely difference plots for the same data. Please
see
the attached
Hi there,
I am encountering a weird problem with a REMD simulation using 4.5.3. The total
simulation is 50ns with 5 replica, and I do in two runs: 25ns and then
continuing to 50ns (walltime queue). The first run is okay, the continue run
(the last 25ns) randomly make some xtc files corrupted
Dear All,
Hope this mail will find you in good health.
I am facing a problem regarding Position restrained dynamics (PR). I have
done Molecular dynamic simulation
(for cytosolic protein) but has not performed PR. So i m little confused if
this effects the results and if yes to what extent it
On 21/11/2010 4:01 AM, pawan raghav wrote:
Dear All,
Hope this mail will find you in good health.
I am facing a problem regarding Position restrained dynamics (PR). I
have done Molecular dynamic simulation
(for cytosolic protein) but has not performed PR. So i m little
confused if this
I am beginner with gromacs. I would like to simulate the behavior of glassy
materials starting with simple Lennard Jones liquid.
please advise me as to how to begin.
a relevent flowchart or tutorial would be of immerse help
thank you very much indeed.
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