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 - 09:00:02 PDT
