[gmx-users] Umbrella Sampling Pull code Problem

[Bogdan Costescu]

On Fri, Aug 31, 2012 at 1:45 PM, Steinbrecher, Thomas (IPC)
<thomas.steinbrecher at kit.edu> wrote:
> However, when I make the following two changes in my input file:
>
> pull_start      = no
> pull_init1      = 1.95
>
> which should (?) amount to an equivalent setup, a very different trajectory results in which the COM distance quickly increases to 2.7 nm and then appears to be restrained there. (Visualization confirms, in the first case, the groups remain in their starting conformation, in the second one, they are pushed appart)

My guess is that you should use -1.95 as pull_init1 (mind the minus
sign) and that the COM distance you measure is actually close to 2.9
nm (which is 1.95*2). g_dist measures a distance which is always
non-negative, however pull_init1 is used as a reference position so
its sign depends on the geometry of pulling.

Cheers,
Bogdan