[gmx-users] Simple gas-phase minimization help
Mark Abraham
mark.j.abraham at gmail.com
Thu Jun 16 22:09:00 CEST 2016
Hi,
We can't help if all we have is the information "does not produce an
output." I suggest doing tutorial material locally before you get involved
with the complexity of a cluster.
Mark
On Thu, 16 Jun 2016 19:01 Tarick E <telbaba1 at gmail.com> wrote:
> I have tried a number of edits to my minim.mdp file for minimization with
> no luck. I can generate a tpr without any errors and initiate a simulation
> via mdrun, but no matter what resources I allocate to it (on a
> supercomputer), I cannot produce an output.
>
> Here's my mdp file. I am trying to minimize the structure that I will then
> feed into an md simulation in vacuum:
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep = 0.001 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list
> and long range forces
> rlist = 0
> cutoff-scheme = group
> ns_type = grid ; Method to determine neighbor list
> (simple, grid)
> coulombtype = cut-off ; Treat all long-range
> electrostatics
> rcoulomb = 0 ; Short-range electrostatic cut-off
> rvdw = 0 ; Short-range Van der Waals cut-off
> pbc = no ; Periodic Boundary Conditions
> (yes/no)
>
>
> Any help is greatly appreciated!
>
> On Wed, Jun 15, 2016 at 4:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 6/15/16 4:46 PM, Tarick E wrote:
> >
> >> Thanks for the help!
> >>
> >> I am following the Lysozyme tutorial except I am not solvating with
> water
> >> or balancing the charge with counter ions. When generating my .tpr with
> >> grompp, I am receiving the error:
> >>
> >> ERROR 1 [file minim_nick_edit1.mdp]:
> >> With Verlet lists only full pbc or pbc=xy with walls is supported
> >>
> >>
> > Then you need cutoff-scheme = group.
> >
> > -Justin
> >
> >
> > I have removed periodic boundary conditions. See my mdp below for a
> simple
> >> minimization:
> >>
> >> title = Energy Minimization ; Title of run
> >>
> >> ; The following line tell the program the standard locations where to
> find
> >> certain files
> >> cpp = /lib/cpp ; Preprocessor
> >>
> >> ; Define can be used to control processes
> >> define = -DFLEXIBLE
> >>
> >> ; Parameters describing what to do, when to stop and what to save
> >> integrator = cg ; Algorithm (cg = conjugate gradient,
> >> steep
> >> = steepest descent minimization)
> >> emtol = 10.0 ; Stop minimization when the maximum
> force
> >> < 1.0 kJ/mol
> >> nstcgsteep = 10 ; ; Frequency of steepest
> descents
> >> steps when doing CG
> >> nsteps = 5000 ; Maximum number of (minimization) steps
> >> to
> >> perform
> >> nstenergy = 1 ; Write energies to disk every nstenergy
> >> steps
> >> energygrps = System ; Which energy group(s) to write to disk
> >>
> >> ; Parameters describing how to find the neighbors of each atom and how
> to
> >> calculate the interactions
> >> nstlist = 0 ; Frequency to update the neighbor list
> >> ns_type = simple ; Method to determine neighbor list
> >> (simple, grid)
> >> rlist = 0
> >> coulombtype = cut-off ; Treatment of long range electrostatic
> >> interactions
> >> epsilon_rf = 78
> >> rcoulomb = 0 ; long range electrostatic cut-off
> >> rvdw = 0 ; long range Van der Waals cut-off
> >> constraints = none ; Bond types to replace by constraints
> >> pbc = no ; Periodic Boundary Conditions (yes/no)
> >>
> >>
> >> On Tue, Jun 14, 2016 at 1:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 6/14/16 1:02 PM, Tarick E wrote:
> >>>
> >>> Hey everyone,
> >>>>
> >>>> I am new to this, so please forgive me if this has been asked before.
> >>>>
> >>>> I am trying to conduct an energy minimization in vacuum on individual
> >>>> proteins and small peptides at a constant temperature, but I am having
> >>>>
> >>>>
> >>> There is no temperature during energy minimization.
> >>>
> >>> trouble with this. Is there any documentation someone can lead me to
> for
> >>>
> >>>> producing a vacuum-phase minimization .mdp file? I have been trying to
> >>>> edit
> >>>> the various .mdp files provided in the Lysozyme tutorial written by
> >>>> Justin
> >>>> Lemkul, but I haven't had any luck and I can't seem to locate any info
> >>>> in
> >>>> the Gromacs users manual.
> >>>>
> >>>>
> >>>> Set all cutoffs to zero and do not use PBC. Then you're in vacuum.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==================================================
> >>>
> >>> 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
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
> >>>
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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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