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

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 27 12:58:49 CEST 2010

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.


> Shahid 
> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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