[gmx-users] Does One need to set comm_mode = none for an equilibrium MD to get exact MSD?

[David van der Spoel]

Hu Zhongqiao wrote:
> 
> 
> Dear all,
> 
>  
> 
> When I run equilibrium MD simulation, I did not do anything for COM 
> removal in .mdp file. So by default, the linear motion of COM of the 
> whole system should be removed. In this case, the MSD calculated by 
> g_msd should be different from that otherwise. So one needs to set 
> comm_mode = none?
> 
no.

comm_mode = linear is fine. Diffusion should be measured independent of 
any overall motion.
>  
> 
> Thanks,
> 
> Zhongqiao
> 
>  
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se