[gmx-users] Gromacs 2016 pull options

[Gmx QA]

Hi Justin

Thank you for your response.

I will test that obviously, but just for my understanding then:
Is it not enough to specify the pull-coord1-rate, you also need the
pull-coord1-k to make it work?

They seem to be specifying sort of the same thing really…

Thanks
/PK

2017-02-20 14:13 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 2/20/17 8:09 AM, Gmx QA wrote:
>
>> Dear list
>>
>> Could someone please clarify a few issues I have with the 2016 version of
>> the pull code. Or rather, explain why the below approach is not working.
>>
>> I am trying to pull a small molecule though a bilayer. Initially, the drug
>> is "below" the membrane, i e has a smaller z-coordinate, so I want to pull
>> in the positive z direction through the membrane.
>>
>> The following is a snippet of my mdp-file, with the relevant parts for the
>> pull specs.
>>
>> pull                      = yes
>> pull-ngroups             = 2
>> pull-ncoords             = 1
>> pull-coord1-groups       = 1 2
>> pull-group1-name         = drug
>> pull-group2-name         = membrane
>> pull-coord1-type         = umbrella
>> pull-coord1-geometry     = direction-periodic
>> pull-coord1-vec          = 0 0 1
>> pull-coord1-rate         = 0.1
>>
>> This I think should define two pull groups,one for the drug and one for
>> the
>> membrane, and it should pull the drug molecule with pull-coord1-rate in
>> positive z. I am using direction-periodic since I expect to pull more than
>> half the box z length.
>>
>> When I test this, running a 1 ns simulation, during which I expect the
>> drug
>> to be pulled a significant way, nothing really happens with the com of the
>> drug, it just "sits" out in the water phase.
>>
>>
> You didn't set a value of pull-coord1-k, so it defaults to zero and
> therefore you get no biasing potential.
>
> http://manual.gromacs.org/documentation/2016.2/user-guide/
> mdp-options.html#com-pulling
>
> -Justin
>
> --
> ==================================================
>
> 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
>
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