Hi Daniel,
Thanks for the reply. However I am getting this problem although I have
already used the unwrap command in ptraj to unfold the trajectory.
Also one more thing that I am observing is that while generating .pdb files
using ptraj with unwrap command, some of atoms attains a very high negative
value (< -1000) for coordinates. For these coordinates "********" appears
in the .pdb file instead of real coordinates. However, this is not the only
reason for getting wrong MSD value as there are some atoms which rather
than showing "********", show wrong coordinates in .pdb file after 60ns.
On Mon, Apr 13, 2015 at 9:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Apr 10, 2015 at 12:20 AM, pooja chahal
> <chahal.pooja.rs.gmail.com> wrote:
> > I have a query regarding the calculation of diffusion constant in ptraj.
> I
> > have performed a NPT simulation of 100ns for a globular protein using
> TIP3P
> > water model. I have also used iwrap=1. For the calculation of diffusion
> > constant I have calculated MSD in two ways:
>
> Note that if you're trying to compare to experimental values you'll
> want to perform simulations in the microcanonical ensemble (NVE) with
> a shorter timestep and increased SHAKE tolerance since
> barostats/thermostats/integrator errors will impact your results.
>
> > I am getting same MSD values using both the methods till 60ns but
> strangely
> > after 60ns some bumps are observed in MSD value calculated using PDB
> files.
> > Overall MSD vs time curve is similar but after 60ns at some points MSD
> > values calculated using PDB files shows very high values. I would
> > appreciate any help.
>
> I suspect what is happening is that you have an orthorhombic unit cell
> and an imaged trajectory. You should add an 'unwrap' command before
> writing out your trajectory to get rid of any imaging issues. If you
> don't when a water is imaged from one side of the box to the other
> this can appear like an instantaneous jump across the box if not
> corrected for, which will artificially inflate your diffusion
> constant. The ptraj diffusion command corrects for periodicity when
> the unit cell is orthorhombic.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Mon Apr 13 2015 - 22:00:02 PDT
