[gmx-users] Energy Conservation at the Beginning of a Production Run
Justin Lemkul
jalemkul at vt.edu
Fri Mar 29 14:00:32 CET 2019
On 3/29/19 4:30 AM, Mark Abraham wrote:
> 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.
I would think any problems that might arise would be minimal, such that
the user can easily recover the original geometry by turning constraints
off and generating a new .tpr file. This could also be a very good
opportunity to notify the user if they are perhaps unwittingly
introducing a discontinuity between unconstrained and constrained
processes, e.g. if the constraint RMSD is larger than some (small)
threshold, we can print a note to alert the user about potential
discontinuities.
-Justin
> 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
>>>>
>>>> * Please search the archive at
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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
>>> --
>>> Gromacs Users mailing list
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>>> * Please search the archive at
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>> send a mail to gmx-users-request at gromacs.org.
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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