[gmx-users] Pull code

[Ming Tang]

Dear Justin,

I want to simulate my triple helix using SMD, Can I use umbrella + distance?  I saw many people doing SMD simulation by fixing one end and pull another end in their journal. Besides, my triple helix deviates a bit from Z axis, but I do not know the angle. I checked both dim for distance and pull-vec for direction, and found both of them needs pull direction. If I set dim = N N Y, will the force-deformation be reliable?

Thanks.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Thursday, 23 April 2015 10:33 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pull code



On 4/22/15 8:03 PM, Ming Tang wrote:
> Hi, Justin
>
> I am confusing about what is the difference between the rigid constraint in constraint pull method and the harmonic potential using umbrella.
> The force acts directly on the centre of mass of the group in constraint, and the force acts on the center of mass of the group through a spring when using umbrella pull method.
> Am I right?

There is of course no difference in the fact that the two groups are restrained between their COM.  The difference comes in how the force is applied and how the positions are updated.  It's just like bonds.  A harmonic bond (connection, restraint, whatever) oscillates about some mean value.  That's the deal with the "umbrella" harmonic restraint.  There is a target value, and the deviation from that target determines the magnitude of the force applied along the restraint vector to give rise to that target.  With the "constraint" method, the positions are updated with SHAKE (as stated in the manual).  A difference vector is calculated between the current position and the target position.  The positions of the groups are then updated along that vector such that the rigid constraint is satisfied.  It's the difference between being connected with a spring and being connected with a lead pipe.

-Justin

>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf 
> Of Justin Lemkul
> Sent: Thursday, 23 April 2015 9:22 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pull code
>
>
>
> On 4/22/15 7:17 PM, Ming Tang wrote:
>> Hi，Alex
>>
>> You can try constraint. In umbrella， both 2 groups move.
>>
>
> Not really.  The constraint option keeps a rigid constraint between the two groups.  The "umbrella" keyword specifies a harmonic potential, whose strength is tunable.  Otherwise, the two methods are identical.
>
> If one group needs to stay in place, it needs position restraints applied to it.
>    If the desired separation is not occurring, either a larger spring force constant or a faster pull rate is needed.
>
> -Justin
>
>> Sent from my Huawei Mobile
>>
>> Alex <nedomacho at gmail.com> wrote:
>>
>> Hi all,
>>
>> I have a group (DNA) I'd like to translate relative to the other 
>> group
>> (CNT) along the Z-direction so that DNA is the only group that's 
>> actually moving.
>>
>> The code I had prior to what I have now worked under GMX 4.5.something.
>> Since the syntax has changed in 5.0.x, I found Justin's old 
>> suggestions, and this is what I have now:
>>
>> ;Pull code
>>
>> pull                = umbrella
>>
>> pull_geometry       = direction
>>
>> pull_coord1_vec     = 0.0 0.0 1.0
>>
>> pull_start          = yes
>>
>> pull_coord1_init    = 0.0
>>
>> pull_ngroups        = 2
>>
>> pull_ncoords        = 1
>>
>> pull_coord1_groups  = 1 2
>>
>> pull_group1_name    = CNT
>>
>> pull_group2_name    = DNA
>>
>> pull_coord1_rate1   = 0.0002          ;nm per ps
>>
>> pull_coord1_k       = 5000          ; kJ mol^-1 nm^-2
>>
>> ;end pull code
>>
>>
>> Does this look right? My simulation isn't nearly done, but I am 
>> looking at the Z-displacement in pullx.xvg and it just oscillates 
>> around a single value. The simulated time is now about 1.5 ns.
>>
>>
>> Thank you,
>>
>>
>> Alex
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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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