[gmx-users] Simple gas-phase minimization help
Tarick E
telbaba1 at gmail.com
Thu Jun 16 22:25:11 CEST 2016
Hi Mark,
Thanks for the reply. I have attempted to run this on Gromacs installed on
a local machine as well as on a cluster. In either case, the simulations
would not complete after being run for ~12 hours. I feel that there is an
error in my mdp file but I am not sure what it could be.
I'm trying to minimize the structure with a net charge of +8 in vacuum and
then conduct simulated annealing in vacuum to determine the low energy
gas-phase equilibrium structures to compare with collisional activation
studies by ion mobility spectrometry.
Thanks again for taking time to help me out.
Sincerely,
Tarick
On Thu, Jun 16, 2016 at 4:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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