[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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list