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-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Thursday, 23 April 2015 9:22 AM
To: gmx-us...@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 <nedoma...@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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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