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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 27 16:15:31 CEST 2010

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.


>> On 4/23/10, *Mark Abraham* <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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