[gmx-users] error in running md
VARSHA RANI
varsha24_sps at jnu.ac.in
Tue Jun 13 14:51:13 CEST 2017
Thanks for reply.
As suggested by Mark Abraham, I ran same calculation for energy
minimization for pentacene single molecule.
minim.mdp is same and screen output is
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 10 in 78 steps
Potential Energy = 1.0244328e+02
Maximum force = 9.6825466e+00 on atom 10
Norm of force = 5.3154244e+00
and the pdb for one molecule of pentacene is as
petacene-pdb
ATOM 1 C1 PE 1 1.247 -0.647 -0.108 1.00 2.95 1PE
ATOM 2 C2 PE 1 0.775 -0.326 1.167 1.00 2.95 1PE
ATOM 3 C3 PE 1 1.477 -0.610 2.344 1.00 2.95 1PE
ATOM 4 C4 PE 1 0.973 -0.271 3.594 1.00 2.95 1PE
ATOM 5 C5 PE 1 1.723 -0.555 4.797 1.00 2.95 1PE
ATOM 6 C6 PE 1 1.242 -0.219 6.006 1.00 2.95 1PE
ATOM 7 C7 PE 1 -0.042 0.431 6.128 1.00 2.95 1PE
ATOM 8 C8 PE 1 -0.769 0.717 5.013 1.00 2.95 1PE
ATOM 9 C9 PE 1 -0.297 0.392 3.691 1.00 2.95 1PE
ATOM 10 C10 PE 1 -1.004 0.678 2.556 1.00 2.95 1PE
ATOM 11 C11 PE 1 -0.516 0.340 1.278 1.00 2.95 1PE
ATOM 12 H1 PE 1 2.068 -1.076 -0.188 1.00 2.95 1PE
ATOM 13 H2 PE 1 2.301 -1.037 2.287 1.00 2.95 1PE
ATOM 14 H3 PE 1 2.549 -0.976 4.732 1.00 2.95 1PE
ATOM 15 H4 PE 1 1.740 -0.406 6.768 1.00 2.95 1PE
ATOM 16 H5 PE 1 -0.373 0.653 6.968 1.00 2.95 1PE
ATOM 17 H6 PE 1 -1.594 1.135 5.108 1.00 2.95 1PE
ATOM 18 H7 PE 1 -1.826 1.106 2.630 1.00 2.95 1PE
ATOM 19 C12 PE 1 -1.247 0.647 0.108 1.00 2.95 1PE
ATOM 20 C13 PE 1 -0.775 0.326 -1.167 1.00 2.95 1PE
ATOM 21 C14 PE 1 -1.477 0.610 -2.344 1.00 2.95 1PE
ATOM 22 C15 PE 1 -0.973 0.271 -3.594 1.00 2.95 1PE
ATOM 23 C16 PE 1 -1.723 0.555 -4.797 1.00 2.95 1PE
ATOM 24 C17 PE 1 -1.242 0.219 -6.006 1.00 2.95 1PE
ATOM 25 C18 PE 1 0.042 -0.431 -6.128 1.00 2.95 1PE
ATOM 26 C19 PE 1 0.769 -0.717 -5.013 1.00 2.95 1PE
ATOM 27 C20 PE 1 0.297 -0.392 -3.691 1.00 2.95 1PE
ATOM 28 C21 PE 1 1.004 -0.678 -2.556 1.00 2.95 1PE
ATOM 29 C22 PE 1 0.516 -0.340 -1.278 1.00 2.95 1PE
ATOM 30 H8 PE 1 -2.068 1.076 0.188 1.00 2.95 1PE
ATOM 31 H9 PE 1 -2.301 1.037 -2.287 1.00 2.95 1PE
ATOM 32 H10 PE 1 -2.549 0.976 -4.732 1.00 2.95 1PE
ATOM 33 H11 PE 1 -1.740 0.406 -6.768 1.00 2.95 1PE
ATOM 34 H12 PE 1 0.373 -0.653 -6.968 1.00 2.95 1PE
ATOM 35 H13 PE 1 1.594 -1.135 -5.108 1.00 2.95 1PE
ATOM 36 H14 PE 1 1.826 -1.106 -2.630 1.00 2.95 1PE
TER
As there is no amino acid in this molecule, I have created a residue
named 'PE'. for this I have edited some files in the 'top' directory
of gromacs. The files are..'residues.types.dat', 'residues.xml',
'refi_aa.dat' and besides that for oplsaa force field, I edited
'aminoacids.rtp' file also.
regards
On Tue, Jun 13, 2017 at 4:57 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Technically this is energy minimization, not md. But likely the energy
> should be negative. It's hard to help because you haven't told us what is
> in the system, but if it's multiple organic molecules, start with one, to
> see if your topology works appropriately.
>
> Mark
>
> On Tue, 13 Jun 2017 12:45 VARSHA RANI <varsha24_sps at jnu.ac.in> wrote:
>
> > Hi,
> >
> > I ran minim.mdp for my system with 3456 atoms. But lowest energy after
> > minimization is positive.
> >
> > *here is th screen output*
> >
> > Step= 4509, Dmax= 4.5e-05 nm, Epot= 4.06554e+02 Fmax= 9.86206e+00, atom=
> > 3521
> >
> > writing lowest energy coordinates.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.1#
> >
> > Steepest Descents converged to Fmax < 10 in 4510 steps
> > Potential Energy = 4.0655389e+02
> > Maximum force = 9.8620596e+00 on atom 352
> > Norm of force = 3.3500545e+00
> >
> > NOTE: 16 % of the run time was spent in pair search,
> > you might want to increase nstlist (this has no effect on accuracy)
> >
> >
> > *Below is txt of minim.mdp file *
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator = steep ; Algorithm (steep = steepest descent
> > minimization)
> > emstep = 0.01 ; Energy step size
> > ;emtol = 1000.0 ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > nsteps = 500000 ; Maximum number of (minimization) steps to
> > perform
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist = 10 ; Frequency to update the neighbor
> > list and long range forces
> > rlist = 2 ; cut-off for making neighbour list (short
> > range forces)
> > cutoff-scheme = Verlet
> > ns_type = grid ; Method to determine neighbor list
> > (simple, grid)
> > coulombtype = PME ; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 0.9 ; Short-range electrostatic cut-off
> > rvdw = 0.9 ; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions (yes/no)
> >
> >
> >
> > regards
> > --
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