[gmx-users] Energy Conservation at the Beginning of a Production Run

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 29 09:30:43 CET 2019 

Hi,

Off topic for this discussion, but what would people think if we changed
things around so that grompp would do that constraining, before writing the
tpr file?

This will mean that the configuration in the tpr does not always match the
configuration that was given to grompp, but instead matches the rest of the
simulation. Thus such an energy jump would not occur. And it may mean that
broken structures are found at grompp time rather than later at step 0 when
doing mdrun on the cluster.

Mark

On Fri., 29 Mar. 2019, 02:17 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 3/28/19 6:02 PM, Kruse, Luke E.(MU-Student) wrote:
> > In the production run I have constraints on h-bonds and I do not have
> any constraints in the minimization.
>
> This would account for a sudden change in energy. At step 0, your H
> positions will immediately change.
>
> -Justin
>
> > ________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van
> der Spoel <spoel at xray.bmc.uu.se>
> > Sent: Thursday, March 28, 2019 4:50:38 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Energy Conservation at the Beginning of a
> Production Run
> >
> > Den 2019-03-28 kl. 21:19, skrev Kruse, Luke E.(MU-Student):
> >> In the mdout.mdp file corresponding to this run I have the line
> >>
> >> ; Do not constrain the start configuration
> >> continuation             = no
> >>
> >>
> >> Do I need to change this to yes?
> > Maybe, try a 100 step run where you save energies at each time step. Did
> > you change anything else between minimization and production, e.g.
> > constraint settings?
> >>
> >> The plot of energy vs time looks like an under damped response to a set
> point change in control theory - slight overshooting after the first few
> steps, then settling down to an average value nicely. This is what is
> leading me to believe that there is a large, non conservative force near
> the beginning that becomes smaller, and conservative.
> >>
> >> Time (ps)
> >>
> >>       0.000000  -1851396.981075
> >>       0.100000  -1851388.994856
> >>       0.200000  -1851390.001591
> >>       0.300000  -1851389.436699
> >>       0.400000  -1851389.760231
> >>       0.500000  -1851389.726310
> >>       0.600000  -1851389.808428
> >>       0.700000  -1851389.907829
> >>       0.800000  -1851389.840644
> >>       0.900000  -1851389.967373
> >>       1.000000  -1851390.061502
> >>       1.100000  -1851390.057500
> >>       1.200000  -1851390.086172
> >>       1.300000  -1851390.042747
> >>       1.400000  -1851390.060210
> >>       1.500000  -1851389.998599
> >>       1.600000  -1851390.120319
> >>       1.700000  -1851390.141846
> >>       1.800000  -1851390.131003
> >>       1.900000  -1851390.170220
> >>       2.000000  -1851390.141617
> >>       2.100000  -1851390.135779
> >>       2.200000  -1851390.255565
> >>       2.300000  -1851390.153947
> >>       2.400000  -1851390.238681
> >>       2.500000  -1851390.144512
> >>       2.600000  -1851390.255200
> >>       2.633000  -1851390.178012
> >>
> >>
> >> ________________________________
> >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van
> der Spoel <spoel at xray.bmc.uu.se>
> >> Sent: Thursday, March 28, 2019 3:10:05 PM
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Energy Conservation at the Beginning of a
> Production Run
> >>
> >> Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student):
> >>> Hello gromacs users,
> >>>
> >>>
> >>> I am trying to simulate a peptide amphiphile with the CHARMM27 force
> field. To do this I have had to specify an additional bond type and bond,
> angle, dihedral, etc. parameters in the .itp files of the force field.
> Then, to check if I had done this correctly, I minimized the system, and
> ran a production run to generate an NVE ensemble, so that I could make sure
> the system was conserving energy appropriately. After looking at the energy
> vs time plot (produces with the gmx energy command), however, the system
> jumps from an initial energy, up ~20 kJ per mole and then conserves energy
> for the most part (slight drifting but seems tolerable relative to the
> initial discontinuity). Is this discontinuity a normal happenstance or a
> result of bad minimization?
> >>>
> >> Is that at step 0 in the simulation?
> >>
> >> Please check options like
> >> ; Do not constrain the start configuration
> >> continuation             = no
> >>
> >>
> >>> Thank you!
> >>>
> >>> Luke
> >>>
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Head of Department, Cell & Molecular Biology, Uppsala University.
> >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> >> http://www.icm.uu.se
> >> --
> >> Gromacs Users mailing list
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> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Head of Department, Cell & Molecular Biology, Uppsala University.
> > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> > http://www.icm.uu.se
> > --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
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>
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