[gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

Many thanks Justin, that’s solved it.

The simulation is now running, reporting that 8 POPC molecules and 12 SOL
molecules have been removed. However, I have a bit of a problem. I don’t
seem to be able to get the -membed option working on a parallel
installation of gromacs, only serial. I assume parallel isn’t supported?

Secondly, with my .tpr file very different from my running .trr (due to
removed molecules), I don’t know of a way of pulling out a single frame
from the trajectory to see how the simulation is progressing. (I would
have just taken the first frame as a .gro, downloaded the latest .trr, and
thrown them both into VMD). Any thoughts?

Many thanks
Anthony 




On 06/01/2016 19:18, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:

>
>
>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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