On 28/04/10 15:13, shahid nayeem wrote:
Hi Mark
How one should be certain that this much  trajectory is long enough to
get coverged ensemble.

When the observables of interest aren't changing... This is a "how long is a piece of string?"-type question. Read some literature about simulations of similar systems. Think many hundreds of nanoseconds, probably.

Mark

On 4/27/10, *Mark Abraham* <mark.abra...@anu.edu.au
<mailto: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>
            <mailto: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>
            <mailto: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>
            <mailto: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
    <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

Reply via email to