[gmx-users] error in running md
Justin Lemkul
jalemkul at vt.edu
Tue Jun 13 14:52:53 CEST 2017
On 6/13/17 8:51 AM, VARSHA RANI wrote:
> 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
>
This is entirely normal. You have a single molecule and no solvent, so in a
case like this, the energy is dominated by internal (bonded) terms, which are
strictly positive. There is no solvent, e.g. water, which is normally dominated
by favorable electrostatic interactions.
-Justin
> 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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--
==================================================
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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