[gmx-users] Gromacs 2016 pull options

[Justin Lemkul]

On 2/20/17 8:24 AM, Gmx QA wrote:
> Ah, ok, so the rate does not specify the velocity by which the pull-group
> moves?
>

No.  Motion of the groups depends on the forces, not the velocity at which the 
virtual spring moves.

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

No, and there are important differences in the way options are specified for 
constant velocity and constant force pulling.  See the link I provided, where 
all of that is described.

-Justin

> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

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