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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of David van der
Spoel <sp...@xray.bmc.uu.se>
Sent: Thursday, March 28, 2019 3:10:05 PM
To: gmx-us...@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
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