[gmx-users] membed in mdrun VERSION 5.0.4

[Justin Lemkul]

On 1/6/16 2:00 PM, Nash, Anthony wrote:
> Hi all,
>
> I thought I would try using the -membed option of mdrun to insert a
> helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions on
> g_membed to generate my required .tpr file. Upon calling grommp I get:
>
> ERROR 1 [file membed_NPT.mdp]:
>    Energy group exclusions are not (yet) implemented for the Verlet scheme
>
>
> My input file can be seen below. If seems as though the Integrator is the
> issue, even though I¹ve picked the correct one. Is a place holder feature?
>

It's not the integrator that's the problem.  It is, as the error states, the use 
of the Verlet cutoff scheme.  Presumably "cutoff-scheme = group" would 
circumvent this issue.

-Justin

> Many thanks
> Anthony
>
> integrator = md
> energygrps = Protein
> freezegrps = Protein
> freezedim = Y Y Y
> energygrp_excl = Protein Protein
>
>
> nsteps          = 5000000       ; 2 * 500000 = 1000 ps (2 ns)
> dt                  = 0.002             ; 2 fs
> nstxout         = 10000         ; save coordinates every 0.2 ps
> nstvout         = 10000         ; save velocities every 0.2 ps
> nstenergy       = 10000         ; save energies every 0.2 ps
> nstlog          = 10000         ; update log file every 0.2 ps
>
> continuation    = yes               ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds             ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter      = 1                         ; accuracy of LINCS
> lincs_order     = 4                         ; also related to accuracy
>
> ns_type         = grid          ; search neighboring grid cels
> nstlist         = 5                 ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
>
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4                 ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
>
> tcoupl          = Berendsen   ;Nose-Hoover                  ; More
> accurate thermostat
> tc-grps         = Protein  POPC SOL     ; three coupling groups - more
> accurate
> tau_t           = 0.5   0.5 0.5                 ; time constant, in ps
> ref_t           = 310   310 310                 ; reference temperature,
> one for each group, in K
>
> pcoupl          = Parrinello-Rahman         ; Pressure coupling on in NPT
> pcoupltype      = semiisotropic             ; uniform scaling of x-y box
> vectors, independent z
> tau_p           = 5.0                           ; time constant, in ps
> ref_p           = 1.0   1.0                     ; reference pressure, x-y,
> z (in bar)
> compressibility = 4.5e-5        4.5e-5  ; isothermal compressibility,
> bar^-1
>
> pbc                 = xyz               ; 3-D PBC
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> gen_vel         = no            ; Velocity generation is off
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = POPC_Protein SOL
> refcoord_scaling = com
>
>

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

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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