[gmx-users] Change to umbrella sampling pull code

[Nash, Anthony]

Hi Mark,

Thanks for the reply.

Comparing the documentation between manual-4.5.6 (what I had previously
been using) and manual-5.0.4:

4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there
is no explicit mention (that I can see) to a reference group but there is
one for the pull group (pull-group1-name).

Thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 12/08/2015 19:35, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

>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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