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

shahid nayeem msnayeem at gmail.com
Tue Apr 27 09:07:13 CEST 2010

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

On 4/23/10, Mark Abraham <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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