[gmx-users] Pull code
m21.tang at qut.edu.au
Thu Apr 23 02:04:05 CEST 2015
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?
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:
> 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.
> 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,
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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
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