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

[Justin Lemkul]

On 3/29/19 12:23 PM, Kruse, Luke E.(MU-Student) wrote:

Thank you all for the help!

Introducing the h-bond constraints into the minimization as well, did reduce 
the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps 
but did not remove the problem entirely. I am also using different 
coulombtype's in the minimization (Cut-off) and the production run (PME). Could 
this be causing the spike, and, is this bad practice? The minimization did not 
converge when I used coulombtype = PME.


Cutoff electrostatics are horribly inaccurate and in and of themselves 
are bad practice. By changing the way the energy of the system is 
calculated between minimization and MD, you should certainly expect a 
difference in the energy. The same coordinates will, by definition, 
yield different energies.


-Justin



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Thursday, March 28, 2019 8:16:34 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production 
Run



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-boun...@maillist.sys.kth.se 
 on behalf of David van der Spoel 

Sent: Thursday, March 28, 2019 4:50:38 PM
To: gmx-us...@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)

   0.00  -1851396.981075
   0.10  -1851388.994856
   0.20  -1851390.001591
   0.30  -1851389.436699
   0.40  -1851389.760231
   0.50  -1851389.726310
   0.60  -1851389.808428
   0.70  -1851389.907829
   0.80  -1851389.840644
   0.90  -1851389.967373
   1.00  -1851390.061502
   1.10  -1851390.057500
   1.20  -1851390.086172
   1.30  -1851390.042747
   1.40  -1851390.060210
   1.50  -1851389.998599
   1.60  -1851390.120319
   1.70  -1851390.141846
   1.80  -1851390.131003
   1.90  -1851390.170220
   2.00  -1851390.141617
   2.10  -1851390.135779
   2.20  -1851390.255565
   2.30  -1851390.153947
   2.40  -1851390.238681
   2.50  -1851390.144512
   2.60  -1851390.255200
   2.633000  -1851390.178012



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der Spoel 

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

Institutionen för cell- och molekylärbiologi - Uppsala 
universitet
www.icm.uu.se
Sanna Koskiniemi får ERC Starting Grant 2018-07-27 Ettemas 

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

[Kruse, Luke E.(MU-Student)]

Thank you all for the help!

Introducing the h-bond constraints into the minimization as well, did reduce 
the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps 
but did not remove the problem entirely. I am also using different 
coulombtype's in the minimization (Cut-off) and the production run (PME). Could 
this be causing the spike, and, is this bad practice? The minimization did not 
converge when I used coulombtype = PME.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Thursday, March 28, 2019 8:16:34 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production 
Run



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-boun...@maillist.sys.kth.se 
>  on behalf of David van 
> der Spoel 
> Sent: Thursday, March 28, 2019 4:50:38 PM
> To: gmx-us...@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)
>>
>>   0.00  -1851396.981075
>>   0.10  -1851388.994856
>>   0.20  -1851390.001591
>>   0.30  -1851389.436699
>>   0.40  -1851389.760231
>>   0.50  -1851389.726310
>>   0.60  -1851389.808428
>>   0.70  -1851389.907829
>>   0.80  -1851389.840644
>>   0.90  -1851389.967373
>>   1.00  -1851390.061502
>>   1.10  -1851390.057500
>>   1.20  -1851390.086172
>>   1.30  -1851390.042747
>>   1.40  -1851390.060210
>>   1.50  -1851389.998599
>>   1.60  -1851390.120319
>>   1.70  -1851390.141846
>>   1.80  -1851390.131003
>>   1.90  -1851390.170220
>>   2.00  -1851390.141617
>>   2.10  -1851390.135779
>>   2.20  -1851390.255565
>>   2.30  -1851390.153947
>>   2.40  -1851390.238681
>>   2.50  -1851390.144512
>>   2.60  -1851390.255200
>>   2.633000  -1851390.178012
>>
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of David van 
>> der Spoel 
>> 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
Institutionen för cell- och molekylärbiologi - Uppsala 
universitet
www.icm.uu.se
Sanna Koskiniemi får ERC Starting Grant 2018-07-27 Ettemas grupp klargör 
mitokondriellt ursprung i Nature journal 2018-05-25 Johanssons och Elfs grupp 
rapporterar om ny metod för 

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

[Justin Lemkul]

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,  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-boun...@maillist.sys.kth.se <

gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of David van
der Spoel 

Sent: Thursday, March 28, 2019 4:50:38 PM
To: gmx-us...@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)

   0.00  -1851396.981075
   0.10  -1851388.994856
   0.20  -1851390.001591
   0.30  -1851389.436699
   0.40  -1851389.760231
   0.50  -1851389.726310
   0.60  -1851389.808428
   0.70  -1851389.907829
   0.80  -1851389.840644
   0.90  -1851389.967373
   1.00  -1851390.061502
   1.10  -1851390.057500
   1.20  -1851390.086172
   1.30  -1851390.042747
   1.40  -1851390.060210
   1.50  -1851389.998599
   1.60  -1851390.120319
   1.70  -1851390.141846
   1.80  -1851390.131003
   1.90  -1851390.170220
   2.00  -1851390.141617
   2.10  -1851390.135779
   2.20  -1851390.255565
   2.30  -1851390.153947
   2.40  -1851390.238681
   2.50  -1851390.144512
   2.60  -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 

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
--
Gromacs Users mailing list

* Please search the archive at

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

[Mark Abraham]

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,  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-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of David van
> der Spoel 
> > Sent: Thursday, March 28, 2019 4:50:38 PM
> > To: gmx-us...@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)
> >>
> >>   0.00  -1851396.981075
> >>   0.10  -1851388.994856
> >>   0.20  -1851390.001591
> >>   0.30  -1851389.436699
> >>   0.40  -1851389.760231
> >>   0.50  -1851389.726310
> >>   0.60  -1851389.808428
> >>   0.70  -1851389.907829
> >>   0.80  -1851389.840644
> >>   0.90  -1851389.967373
> >>   1.00  -1851390.061502
> >>   1.10  -1851390.057500
> >>   1.20  -1851390.086172
> >>   1.30  -1851390.042747
> >>   1.40  -1851390.060210
> >>   1.50  -1851389.998599
> >>   1.60  -1851390.120319
> >>   1.70  -1851390.141846
> >>   1.80  -1851390.131003
> >>   1.90  -1851390.170220
> >>   2.00  -1851390.141617
> >>   2.10  -1851390.135779
> >>   2.20  -1851390.255565
> >>   2.30  -1851390.153947
> >>   2.40  -1851390.238681
> >>   2.50  -1851390.144512
> >>   2.60  -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 
> >> 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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >>
> >> * Can't post? Read 

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

[Justin Lemkul]

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-boun...@maillist.sys.kth.se 
 on behalf of David van der Spoel 

Sent: Thursday, March 28, 2019 4:50:38 PM
To: gmx-us...@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)

  0.00  -1851396.981075
  0.10  -1851388.994856
  0.20  -1851390.001591
  0.30  -1851389.436699
  0.40  -1851389.760231
  0.50  -1851389.726310
  0.60  -1851389.808428
  0.70  -1851389.907829
  0.80  -1851389.840644
  0.90  -1851389.967373
  1.00  -1851390.061502
  1.10  -1851390.057500
  1.20  -1851390.086172
  1.30  -1851390.042747
  1.40  -1851390.060210
  1.50  -1851389.998599
  1.60  -1851390.120319
  1.70  -1851390.141846
  1.80  -1851390.131003
  1.90  -1851390.170220
  2.00  -1851390.141617
  2.10  -1851390.135779
  2.20  -1851390.255565
  2.30  -1851390.153947
  2.40  -1851390.238681
  2.50  -1851390.144512
  2.60  -1851390.255200
  2.633000  -1851390.178012



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der Spoel 

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
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.



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

[Kruse, Luke E.(MU-Student)]

In the production run I have constraints on h-bonds and I do not have any 
constraints in the minimization.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der 
Spoel 
Sent: Thursday, March 28, 2019 4:50:38 PM
To: gmx-us...@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)
>
>  0.00  -1851396.981075
>  0.10  -1851388.994856
>  0.20  -1851390.001591
>  0.30  -1851389.436699
>  0.40  -1851389.760231
>  0.50  -1851389.726310
>  0.60  -1851389.808428
>  0.70  -1851389.907829
>  0.80  -1851389.840644
>  0.90  -1851389.967373
>  1.00  -1851390.061502
>  1.10  -1851390.057500
>  1.20  -1851390.086172
>  1.30  -1851390.042747
>  1.40  -1851390.060210
>  1.50  -1851389.998599
>  1.60  -1851390.120319
>  1.70  -1851390.141846
>  1.80  -1851390.131003
>  1.90  -1851390.170220
>  2.00  -1851390.141617
>  2.10  -1851390.135779
>  2.20  -1851390.255565
>  2.30  -1851390.153947
>  2.40  -1851390.238681
>  2.50  -1851390.144512
>  2.60  -1851390.255200
>  2.633000  -1851390.178012
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of David van 
> der Spoel 
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
>


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

[David van der Spoel]

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)

 0.00  -1851396.981075
 0.10  -1851388.994856
 0.20  -1851390.001591
 0.30  -1851389.436699
 0.40  -1851389.760231
 0.50  -1851389.726310
 0.60  -1851389.808428
 0.70  -1851389.907829
 0.80  -1851389.840644
 0.90  -1851389.967373
 1.00  -1851390.061502
 1.10  -1851390.057500
 1.20  -1851390.086172
 1.30  -1851390.042747
 1.40  -1851390.060210
 1.50  -1851389.998599
 1.60  -1851390.120319
 1.70  -1851390.141846
 1.80  -1851390.131003
 1.90  -1851390.170220
 2.00  -1851390.141617
 2.10  -1851390.135779
 2.20  -1851390.255565
 2.30  -1851390.153947
 2.40  -1851390.238681
 2.50  -1851390.144512
 2.60  -1851390.255200
 2.633000  -1851390.178012



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der Spoel 

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

[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?


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)

0.00  -1851396.981075
0.10  -1851388.994856
0.20  -1851390.001591
0.30  -1851389.436699
0.40  -1851389.760231
0.50  -1851389.726310
0.60  -1851389.808428
0.70  -1851389.907829
0.80  -1851389.840644
0.90  -1851389.967373
1.00  -1851390.061502
1.10  -1851390.057500
1.20  -1851390.086172
1.30  -1851390.042747
1.40  -1851390.060210
1.50  -1851389.998599
1.60  -1851390.120319
1.70  -1851390.141846
1.80  -1851390.131003
1.90  -1851390.170220
2.00  -1851390.141617
2.10  -1851390.135779
2.20  -1851390.255565
2.30  -1851390.153947
2.40  -1851390.238681
2.50  -1851390.144512
2.60  -1851390.255200
2.633000  -1851390.178012



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der 
Spoel 
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
--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

[David van der Spoel]

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 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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mail to gmx-users-requ...@gromacs.org.

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

[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?


Thank you!

Luke
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