[gmx-users] Change to umbrella sampling pull code

[Mark Abraham]

Hi,
On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Dear all,
>
> This is the first time I¹ve ran pull code (for umbrella sampling) since
> the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in
> the .mdp key-value parameters. Could I have a sanity check on the values
> below.


I have no real idea, but you could start by comparing the respective
documentation. If something's not clear, that's something to fix ;-)

Also, given that I want a harmonic potential between the two
> groups, does it matter which index group is assigned to the respective
> Œpull-groupN-name¹ key?
>

I doubt it, but if you want a definitive answer, make yourself a toy test
case and see.

Mark


> Note: my reaction coordinate was defined initially following the
> trajectory between two minima during a meta-dynamics MD simulation. That
> too was distance based.
>
>
> ;Pull code
> pull            = umbrella
> pull-geometry   = distance
> pull-dim        = Y Y Y
> pull-start      = yes
> pull-ngroups    = 1
> pull-group1-name = ZINC
> pull-group2-name = CARBONYL
> pull-coord1-init = 0
> pull-coord1-rate = 0
> pull-coord1-k = 1000
> pull-nstxout    = 1000      ; every 2 ps
> pull-nstfout    = 1000      ; every 2 ps
>
>
> Many thanks
> Anthony
>
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