[gmx-users] Fwd: Regarding correct way to calculate diffusion constant

[Apramita Chand]

---------- Forwarded message ----------
From: Apramita Chand <apramita.chand at gmail.com>
Date: Fri, Aug 26, 2016 at 6:56 PM
Subject: Regarding correct way to calculate diffusion constant
To: gmx-users at gromacs.org


Dear All,
I want to calculate the diffusion constant of urea in my system. I used
g_msd  for this purpose and the value came to be 8.279e -08 (+/-8.85e-09)
1e -5 cm^2/s. Since the value is quite low, I wanted it to check it with
result from VACF.

Any explanations as to why g_msd yielded a low value for a system
conatining 5 urea,751 water and a single protein molecule?

 I ran the calculations again using 17 urea,791 water and protein. The
value comes out to be negative with the same exponent as mentioned above
for urea diffusion. The water diffusion values seem to be normal . I
generated the movie for the trajectory and  urea certainly has movement
though the molecules never wander much from their positions.  In
addition,the radial distribution functions generated for protein-urea shows
site-site interactions but the tail of the g(r) stops short at around 3 A
and does not extend to the bulk(higher distances). What could be wrong in
the simulation?
I'm using GROMACS 4.5.7 and  GROMOS 53a6 parameters. PLease help


Thanking you,
yours sincerely,
Apramita Chand