[gmx-users] the pull code

[Justin Lemkul]

On 8/9/16 2:33 AM, diana p wrote:
> Dear all
>
> I am using the pull code in Gromacs 4.6.5 to calculate the PMF in one
> direction (z) between two graphene sheets in the inter-sheet separation ,
> ranging from 5.0 to 0.3 nm. I run EM and NPT by using .mdp files. When i
> run the  continuous pulling simulation, i seen they are at the current
> location and no movement towards each other!
> The pull parameters are the following:
>
> ;Pull code
>
> pull = umbrella
>
> pull_geometry = direction_periodic   ; simple distance increase
>
> pull_dim = N N Y
>
> pull_start = yes       ; define initial COM distance > 0
>
> pull_ngroups = 1
>
> pull_group0 = GRA 1
>
> pull_group1 = GRA 2
>
> pull_rate1 = 0.01      ; 0.01 nm per ps = 10 nm per ns
>
> pull_k1 = 1000      ; kJ mol^-1 nm^-2
>
>
> I would be more than pleased if someone could guid me.
> Thank You in advance
>

What is the initial separation reported by grompp?  How long is your run?  What 
is in your *full* .mdp file?

-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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