[gmx-users] In vacuo MD

[Mark Abraham]

Hi,

Check again the mdp options. Zero may not be the right choice for all of
them

Mark

On Thu, 15 Jun 2017 13:56 Linus Johannissen <
Linus.Johannissen at manchester.ac.uk> wrote:

> Thanks Justin,
>
> I'm using Gromacs 4.6.1. I don't think changing energygrps is going to
> change anything as I have the same problem in the energy minimisation (zero
> LJ (SR) and Coulomb (SR) energies). However, I found that if the simulation
> seems to run fine if I use a cutoff of 999 instead of 0. To me that should
> be the same, but is there any reason why I should not do that?
>
> Linus
> ___________________
> Dr Linus Johannissen
> Computational Chemistry Experimental Officer
> Manchester Institute of Biotechnology
> University of Manchester
> UK
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin
> Lemkul [jalemkul at vt.edu]
> Sent: 14 June 2017 21:57
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] In vacuo MD
>
> 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
> >
>
> --
> ==================================================
>
> 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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