Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. Shahid
On 4/27/10, Mark Abraham <mark.abra...@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.abra...@anu.edu.au >>> <mailto:mark.abra...@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 >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> 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-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >> -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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