[gmx-users] Gromacs 2016 pull options

[Justin Lemkul]

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

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