[gmx-users] Umbrella sampling

[Justin Lemkul]

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

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================