[gmx-users] Change to umbrella sampling pull code

[Justin Lemkul]

On 8/12/15 3:20 PM, Nash, Anthony wrote:
> 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).
>

Right, because multiple reaction coordinates can now be simultaneously be 
restrained.  There is no requirement for a single reference group.  Any 
combination of groups can be used.  Offhand, your settings are right except 
pull-ngroups is 2, as there are two groups.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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