Hi,
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:
(i) Using ptraj diffusion command. ptraj.in file is as follows
trajin traj1
trajin traj2
diffusion :WAT.O 2.0 average
(ii) Initially I used ptraj to print output of my trajectory in PDB format
and then using pdb files I calculated MSD by writing FORTRAN code. The
ptraj.in file for the geneartion of PDB files is as follow
trajin traj1
trajin traj2
trajout x.out pdb nobox
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.
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Received on Thu Apr 09 2015 - 23:30:02 PDT
