[gmx-users] more than one peptide in one simulation box

[Mark Abraham]

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.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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.Abraham at anu.edu.au
>             <mailto:Mark.Abraham at anu.edu.au>
>             <mailto:Mark.Abraham at anu.edu.au
>             <mailto:Mark.Abraham at 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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