[gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

[Victor Ma]

hello,

I tried various setting of the pull code. But my ligand stays there
intact!!! Here is my pull code:
pull            = umbrella
pull-dim        = Y Y Y
pull-start      = yes       ; define initial COM distance > 0
pull-ngroups    = 2
pull-ncoords    = 1
pull-coord1-groups   = 1 2
pull-group1-name     = Site
pull-group2-name     = LIG
pull-coord1-rate      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k         = 1000      ; kJ mol^-1 nm^-2
pull-geometry = direction-periodic

Can anyone please give any suggestion?
Thank you!!!


Victor

On Wed, Aug 26, 2015 at 11:12 AM, Victor Ma <victordsmagift at gmail.com>
wrote:

> Thank you, Justin! Let me try.
>
> Cheers,
> Victor
>
> On Wed, Aug 26, 2015 at 10:57 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/26/15 1:55 PM, Victor Ma wrote:
>>
>>> Thanks James and Justin!
>>> My target is a big membrane protein. So far i've been using charmm-gui to
>>> set up my simulations. And for the movie, I need to keep the lipids. So
>>> with a charmm-gui pre-setup, can I still implement the "pull code"
>>> easily?
>>>
>>>
>> The advice given does not depend on whether or not there are lipids.
>> It's very simple to position the ligand in some straight line along which
>> you pull it.
>>
>> -Justin
>>
>>
>> Thanks!!!
>>>
>>> Victor
>>>
>>> On Wed, Aug 26, 2015 at 10:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 8/26/15 1:47 PM, Barnett, James W wrote:
>>>>
>>>> Look into the pull code. You'll want to choose two groups (one for the
>>>>> ligand, one for the binding site), and one coordinate with those groups
>>>>> where the pull rate is not zero (negative rate to bring them together,
>>>>> positive rate to pull them apart).
>>>>>
>>>>>
>>>>> And if the purpose is just some cute movie that is not necessarily
>>>> scientifically relevant (shakes head sadly), restrain the protein in
>>>> some
>>>> way to avoid the inherent problem of "hitting a moving target."
>>>>
>>>> -Justin
>>>>
>>>>
>>>> --
>>>>
>>>>> James “Wes” Barnett, Ph.D. Candidate
>>>>> Louisiana Board of Regents Fellow
>>>>> Chemical and Biomolecular Engineering
>>>>>
>>>>> Tulane University
>>>>> 341-B Lindy Boggs Center for Energy and Biotechnology
>>>>> 6823 St. Charles Ave
>>>>> New Orleans, Louisiana 70118-5674
>>>>> jbarnet4 at tulane.edu
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Victor
>>>>> Ma <victordsmagift at gmail.com>
>>>>> Sent: Wednesday, August 26, 2015 12:31 PM
>>>>> To: gmx-users at gromacs.org
>>>>> Subject: [gmx-users] what's the easiest way to generate a md trajectory
>>>>> for ligand flying into/being pulled out of the pocket?
>>>>>
>>>>> hello all
>>>>>
>>>>> I got a urgent request to make a MD movie for pulling the ligand out of
>>>>> the
>>>>> binding site/or the ligand flying into the pocket . I feel like i need
>>>>> to
>>>>> run something like steered md, which I've never done before. So can
>>>>> anyone
>>>>> please suggest a quick and "dirty" way to generate such a movie?
>>>>>
>>>>> Thank you!!
>>>>>
>>>>> Victor
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
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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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>
>