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

Kruse, Luke E.(MU-Student) lekyr8 at mail.missouri.edu
Thu Mar 28 21:19:38 CET 2019

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?

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.
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