[gmx-users] Pulling COM option

[Angela Marcela Murcia Rios]

I have already used enforced rotation to move gamma and yes it works good but now I want to just pull gamma a certain direction just by pulling it and see how the system reacts to this kind of force. I want to understand if it is possible to do this with the pulling COM option of GROMACS and how I would specify this with my system.


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: June 13, 2017 2:15:07 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pulling COM option



On 6/13/17 1:58 PM, Angela Marcela Murcia Rios wrote:
> Hi Justin,
>
>
> I don't want two opposing forces acting on gamma and I don't want to apply it to all of gamma only a specific region, which is what enforced rotation will do. I only want to apply one directional force onto one side of gamma and see how the whole system behaves. But the problem I'm facing is how do I specify this in my mdp file.
>
>

Caveat: I have never used the enforced rotation feature.

But in reading the manual, the fixed axis option says it is applying a torque to
the specified atoms relative to an axis.  Isn't this exactly what you want?
It's not like attaching a spring between groups A and B, you're rotating group A
relative to an axis that you specify.

-Justin

>
> ---Angela
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: June 13, 2017 1:50:35 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pulling COM option
>
>
>
> On 6/13/17 1:48 PM, Angela Marcela Murcia Rios wrote:
>> Hi,
>>
>>
>> I'm not really intersected in the information that the Pulling COM option provides. I am really just interested in getting my protein move in a specific direction until it completes a full circle.
>>
>>
>> To be more specific my system is F1 ATPase and I just want to pull the gamma subunit until it it completes a full circle. I am completely aware that there is an "enforced rotation" option on GROMACS but this is a torque force, which I don't want to use.
>>
>
> Why not?  That's sort of the definition of torque, after all.
>
> -Justin
>
>>
>>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nikhil Maroli <scinikhil at gmail.com>
>> Sent: June 13, 2017 1:03:03 PM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: Re: [gmx-users] Pulling COM option
>>
>> Hi,
>> Out of curiosity, i wanted to ask you what information you will get by rotating
>> protein by 360 degrees.?
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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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--
==================================================

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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