[gmx-users] more than one peptide in one simulation box
msnayeem at gmail.com
Wed Apr 28 07:13:12 CEST 2010
How one should be certain that this much trajectory is long enough to get
On 4/27/10, Mark Abraham <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
>> 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
>>> 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
>>> minimization (steepest descent) failed to converge even after
>>> 5000 steps
>>> and theirafter position restraint dynamics failed giving
>>> 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 :-)
>>> -- gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> Please search the archive at http://www.gromacs.org/search before
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users