[gmx-users] Pull code

[Ming Tang]

Hi， Justin
I will try whether i can set reference group using umbrella later.

Sent from my Huawei Mobile

Justin Lemkul <jalemkul at vt.edu> wrote:



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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