[gmx-users] In vacuo MD

[Justin Lemkul]

On 6/14/17 4:36 AM, Linus Johannissen wrote:
> I'm trying to run an in vacuo MD simulation using infinite non-bonding cutoffs, but Gromacs doesn't seem to be calculating the non-bonding interactions - the protein unfolds very rapidly and in the log file the LJ (SR) and Coulomb (SR) values are 0. Does it look like there's something wrong with my mdp file (below), or is it likely to be something else?
> 

This is how it should be done.  Which version is this?  Is there any difference 
if you specify "System" instead of "Protein" for the energygrps (practically, 
there shouldn't be, but you never know).

-Justin

> Thanks for your help
> Linus
> 
> mdp file:
> 
> title       =  Gas-phase protein simulation
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000    ; 2 * 50000 = 100 ps
> dt          = 0.001    ; 1 fs
> ; Output control
> nstxout     = 0         ; suppress .trr output
> nstvout     = 0         ; suppress .trr output
> nstenergy   = 1000      ; save energies every 1 ps
> nstlog      = 1000      ; update log file every 1 ps
> nstxtcout   = 5000      ; write .xtc trajectory every 5 ps
> energygrps  = Protein
> ; Bond parameters
> continuation    = no           ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = hbonds     ; H-bonds constrained
> lincs_iter      = 2             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> 
> comm-mode = angular
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> cutoff-scheme = group
> vdw-type    = Cutoff
> nstlist     = 0
> ns_type     = simple
> pbc         = no
> rlist       = 0
> coulombtype              = cutoff
> rcoulomb-switch          = 0
> rcoulomb                 = 0
> rvdw                     = 0
> rvdw-switch              = 0
> 
> ; Temperature coupling
> tcoupl      = v-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein
> tau_t       = 0.1                          ; time constant, in ps
> ref_t       = 300                            ; reference temperature
> ; Pressure coupling
> pcoupl      = no        ; no pressure coupling in NVT
> ; Dispersion correction
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
> 
> 
> ___________________
> Dr Linus Johannissen
> Computational Chemistry Experimental Officer
> Manchester Institute of Biotechnology
> University of Manchester
> UK
> 

-- 
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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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