[gmx-users] diffusion coefficient

[Florian Dommert]

Hi,

 you already have your solution at hand.

On 10.02.2010, at 10:05, Amit Choubey wrote:

> Hi Everyone,
> 
> I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers.
> I am using SPCE water model. I use the g_msd analysis tool.
> 
> g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 
> 
> I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get 
> 
> a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/- 0.2992) 1e-5 cm^2/s
> b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/- 0.1076) 1e-5 cm^2/s
> c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s .
> 
> c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but its not quite right. 
> 

You obtain a quite good estimation of the diffusion coefficient when not applying the Berendsen coupling scheme. The reason for this is that Berendsen coupling does not allow to generate a correct thermodynamic ensemble. Applying v-rescale or Nose-Hoover in combination with Parrinello-Rahman should yield more accurate results, because the take the way of sampling the phase space in an appropriate manner into account.

Cheers,

Flo


> Could someone explain to me why the values obtained in above 3 cases are widely different and may be give some tips about the right procedure to calculate diffusion (method and invoking the g_msd tool)? 
> 
> Thank you
> Amit
> 
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658 

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100210/942f1dd3/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PGP.sig
Type: application/pgp-signature
Size: 194 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100210/942f1dd3/attachment.sig>