[gmx-users] Gromacs 2016 pull options

[Gmx QA]

Ah, ok, so the rate does not specify the velocity by which the pull-group
moves?

Does it have the same function in the case of constant-force pulling?

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

>
>
> On 2/20/17 8:19 AM, Gmx QA wrote:
>
>> 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…
>>
>>
> The rate is the velocity at which the biasing spring extends.  The force
> constant calculates how much force is thus applied to the restrained groups
> based on that displacement.  They are independent of one another,
> functionally and mathematically.
>
> -Justin
>
>
> 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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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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