[gmx-users] problem with pull code

[Justin Lemkul]

On 7/12/16 9:47 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-start       = yes         ; define initial COM distance > 0
>>>
>>> ============
>>>
>>> Any guess on the reason? Many thanks.
>>>

Repeatedly posting the same question is not going to increase your odds of an 
answer.  Clearly no one has any ideas.  So try something new to diagnose what's 
going on - a simulation of a single lipid in vacuo with those settings, then 
just one lipid in the bilayer restrained, etc. to see what you can observe. 
Report back with new information, new diagnostics, etc. to make some progress. 
But what you're reporting is basically "something worked and then it didn't," so 
it's hard to give any useful advice.

-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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