[gmx-users] lipid pulling

[Justin Lemkul]

On 7/6/16 7:24 AM, xy21hb wrote:
> Dear all,
>
> I am pulling the saturated and unsaturated chains of a lipid bilayer to "simulate" its gel phase transition by pull code. It ends with the expected extended structure.
>
> But when I continue with zero pulling rate
> to maintain the extended structure for a while, the tails go back to the original length.
> I guess I have made some mistakes in the mdp pull code part,
>
> =========
> pull                    = umbrella
> pull-ngroups            = 6
> pull-ncoords            = 4
>
> pull-group1-name        = topC2
> pull-group2-name        = downC2
> pull-group3-name        = topC218
> pull-group4-name        = downC218
> pull-group5-name        = topC316
> pull-group6-name        = downC316
>
> pull-geometry    = distance      ; simple distance increase
>
> pull-coord1-groups      = 1 3
> pull-coord2-groups      = 1 5
> pull-coord3-groups      = 2 4
> pull-coord4-groups      = 2 6
> pull-dim         = N N Y
>
> pull-coord1-vec         = 0 0 1
> pull-coord1-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k           = 1000          ; kJ mol^-1 nm^-2
> pull-coord2-vec         = 0 0 1
> pull-coord2-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
> pull-coord2-k           = 1000          ; kJ mol^-1 nm^-2
> pull-coord3-vec         = 0 0 1
> pull-coord3-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
> pull-coord3-k           = 1000          ; kJ mol^-1 nm^-2
> pull-coord4-vec         = 0 0 1
> pull-coord4-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
> pull-coord4-k           = 1000          ; kJ mol^-1 nm^-2
>
> pull-coord1-init        =  1.0
> pull-coord2-init        =  1.0
> pull-coord3-init        =  1.0
> pull-coord4-init        =  1.0
>
> pull-start       = yes         ; define initial COM distance > 0
>
> ============
>
> Any guess on the reason? Many thanks.
>

You should use pull-start = yes and not use pull-coord*-init if the lipids are 
already in the configuration you want.  Otherwise, you're trying to set the 
starting distance + 1.0 nm as the reference, which may not be physically 
possible or sensible.

-Justin

-- 
==================================================

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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