On 28/04/10 15:13, shahid nayeem wrote:
Hi Mark
How one should be certain that this much trajectory is long enough to
get coverged ensemble.
When the observables of interest aren't changing... This is a "how long
is a piece of string?"-type question. Read some literature about
simulations of similar systems. Think many hundreds of nanoseconds,
probably.
Mark
On 4/27/10, *Mark Abraham* <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:
shahid nayeem wrote:
Dear Mark
Following your advice I started using three peptide in one
simulation
box. Iwas able to add these with genconf as previously in
ordered
manner, generated .gro with genconf, solvated it and after
energy
minimization I did MD run for 10ns. Everything ran well. In
the end
when I see the trajectory I find unfolding of the original
chain but
the two additional peptide introduced through genconf show
appearance
of new secondary structures. Even in these two the secondary
structure
do not develop at the same point. Why the three equivalent
peptide
behave differently in similar environment. How can I explain
this
observation. why the first peptide does not show any new
secondary
structure. Sholud I go with higher number of molecule. Will
it make
any difference if peptides are added in disordered manner
and then
simulated.
Initial orientation should likely have nothing to do with it.
Perhaps
this is even the proper behavior for whatever your peptide is.
Is its
structure dynamic? Is the size of your peptides large enough to even
believe that they would be intrinsically stable? Many model
peptides, in
isolation, have very transient structures.
It could also be that your simulation parameters are poorly
chosen, so
the force field is breaking down. If you want comments on your .mdp
file, please post it.
Indeed. MD is chaotic, and there's no reason to expect all peptides
of any length to show the same actual behaviour in a trajectory.
They might show the same behaviour in the limit of a converged
ensemble, but only if aggregation is not a factor.
Mark
On 4/23/10, *Mark Abraham* <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 23/04/10 13:16, shahid nayeem wrote:
Dear All
I am trying to study inter peptide interaction fpr which I need
to put
more than one peptide in one simulation box. I did it with
genconf
command but this inserts peptide in a regular ordered manner
I want
these to be in irregular disordered insertion. Even after using
genconf
Well that's a difficult and atypical scenario. genconf
-shuffle will
allow you to stack the same peptide in a regular array with
random
rotations of the whole box. Then you can solvate,
equilibrate and
run MD at a high temperature to give yourself a quasi-disordered
starting state.
, I tried to proceed furthe after solvation with spc water. The
energy
minimization (steepest descent) failed to converge even after
5000 steps
and theirafter position restraint dynamics failed giving
segmentation
fault. Introducing more peptide after generating .gro with
-ci -nmol
gives error showing more than one residue in insert molecule.
Please help me and write commands which I should follow.
No, because that's an impossible task. We can't begin to
guess the
reasons for things failing without seeing the actual output
(was the
EM energy large and negative? what was the actual error message
from -ci -nmol?).
You should be careful to start with a small test case so
that you
can learn the workflow with a manageable problem. Can you get a
single peptide to equilibrate? Two stacked peptides? It is
best to
learn to walk before trying to run :-)
Mark
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