[gmx-users] Umbrella sampling

Justin Lemkul jalemkul at vt.edu
Sun Dec 3 23:25:36 CET 2017

On 12/3/17 8:42 AM, rose rahmani wrote:
> I need to share you sth which just happened;
> i run md_pull.mdp in two steps:
>   1--1nS( dt= 0.001 nsteps=1000000) ,
>   2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
> dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001 nsteps=4000000)
> and The protein was in normal shape in EVERY steps!
> BUT as i told you before when i run just once in 2nS (dt=0.001
> nsteps=2000000) periodic boundary conditions make the protein look unusual
> in for example conf1500.gro?!!!
> What happened? I've got really confused?

Read a bit about periodic boundary conditions and what they mean. This 
is normal behavior.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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