[gmx-users] Umbrella pulling Drug + Ion channel

[Justin Lemkul]

On 3/24/14, 8:56 PM, Andres Ortega wrote:
> Dear gromacs users, i ´ve beem trying to get the geometries of a drug
> molecule permeating an ion channel,
> the drug molecule is in a greater Z position than the Protein, but i always
> get the error :"Segmentation fault (core dumped)"

Does the simulation crash without using the pull code?

> this is my .mdp
>
> title       = Umbrella pulling simulation DOX
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 500 ps
> nstcomm     = 10
> ; Output parameters
> nstxout     = 5000      ; every 10 ps
> nstvout     = 5000
> nstfout     = 500
> nstxtcout   = 500       ; every 1 ps
> nstenergy   = 500
>
> cutoff-scheme = Verlet
>
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes             ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist     = 20
> ns_type     = grid
> rlist       = 1.2
> rcoulomb    = 1.2
> rvdw        = 1.2
> ; PME electrostatics parameters
> coulombtype     = PME
> fourierspacing  = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl      = Nose-Hoover
> tc_grps     = Protein  POPC Water_and_ions_DOX
> tau_t       = 1.0    1.0   1.0
> ref_t       = 310    310   310
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = semiisotropic
> tau_p           = 1.0
> compressibility = 4.5e-5 4.5e-5
> ref_p           = 1.0   1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel     = no
> ; Periodic boundary conditions are on in all directions
> pbc     = xyz
> ; Long-range dispersion correction
> DispCorr    = EnerPres
> ; Pull code
> pull            = umbrella
> pull_geometry   = cylinder  ;
> pull_vec1       = 0.0 0.0 1.0 ;
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = DOX
> pull-r1 = 1.0
> pull-r0 = 1.0
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 800      ; kJ mol^-1 nm^-2
> pull_pbcatom0   = 8485
>
> According with other post, i have to select a pull_pbcatom0 closes to the
> middle of my reference ( an atom close to the middle of the ion channel's
> pore) and a pull_vec1 positive even if the drug is "above" the channel, i
> was wondering if you could help me with this, or giving me an advice of this
> error, thanks in advance
>

pull_pbcatom0 is not relevant here.  It's used to determine periodic distances, 
and only in certain cases.  In fact, if you read the manual entry for it, you 
will note:

"This parameter is not used with geometry cylinder."

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================