VOTCA interpretation units dump file

[Cecília Álvares]

Hello,

I am using a trajectory in the .dump format to derive CG potentials using FM. My dump file contains 8 columns (atom ID, atom type, the three coordinates, the force components in each of the three directions). 

When doing some tests, I came to realize that if I feed VOTCA with a .dump trajectory file containing unscaled coordinates in angstroms, it gives me the same result as if I had fed it the scaled coordinates. So I suppose in its internal script, VOTCA has as the standard unit of the unscaled coordinates in a .dump file to be angs (right?). I was wondering if VOTCA has a special default unit for the forces that are in the .dump file. What is VOTCA going to interpret the unit of the force components as? Something like kJ/(mol.angs) maybe?

[Cecília Álvares]

PS: I am talking about the units in the .force output files (i.e., the ones we obtain by simply doing the csg_fmatch command, with no further commands) and considering that there is no unit conversion information in my fmatch.xml file.

[Christoph Junghans]

On Thu, Jul 27, 2023 at 11:41 AM Cecília Álvares
<cecilia...@gmail.com> wrote:
>
> PS: I am talking about the units in the .force output files (i.e., the ones we obtain by simply doing the csg_fmatch command, with no further commands) and considering that there is no unit conversion information in my fmatch.xml file.

Yes, we use the same unit system as gromacs:
https://manual.gromacs.org/documentation/2019/reference-manual/definitions.htm,
so kJ mol−1 nm−1 for the forces.
But we also assume the positions are in Ang, so there might be a
factor 10 somewhere.
https://github.com/votca/votca/blob/master/csg/src/libcsg/modules/io/lammpsdumpreader.cc#L217
and we assume the forces in the dump file are in kcal/ang.
https://github.com/votca/votca/blob/master/csg/src/libcsg/modules/io/lammpsdumpreader.cc#L243

if that isn't the case for your dump you will need to apply some
scaling factor to the .force file afterwards.

>
> Em quinta-feira, 27 de julho de 2023 às 19:39:19 UTC+2, Cecília Álvares escreveu:
>>
>> Hello,
>>
>> I am using a trajectory in the .dump format to derive CG potentials using FM. My dump file contains 8 columns (atom ID, atom type, the three coordinates, the force components in each of the three directions).
>>
>> When doing some tests, I came to realize that if I feed VOTCA with a .dump trajectory file containing unscaled coordinates in angstroms, it gives me the same result as if I had fed it the scaled coordinates. So I suppose in its internal script, VOTCA has as the standard unit of the unscaled coordinates in a .dump file to be angs (right?). I was wondering if VOTCA has a special default unit for the forces that are in the .dump file. What is VOTCA going to interpret the unit of the force components as? Something like kJ/(mol.angs) maybe?
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Cecília Álvares]

Hey Christoph,

But in fact, even if my forces in the dump file are saved in kcal/(mol.ang), the unit for the force output in the .force files is in kJ/(mol.nm)? Is that it?

[Cecília Álvares]

Aaaaaand upon judging the mathematical formalism of force matching (e.g. the tiny portion below extracted from VOTCA's official paper of 2009), I suppose that VOTCA is outputting in the .force file the function I underlined in blue below. So the units of the force in the case of the angle force-fields should be kJ/(mol.rad), correct?

[Christoph Junghans]

On Fri, Jul 28, 2023, 01:40 Cecília Álvares <cecilia...@gmail.com> wrote:

Hey Christoph,

But in fact, even if my forces in the dump file are saved in kcal/(mol.ang), the unit for the force output in the .force files is in kJ/(mol.nm)? Is that it?

Correct!

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/9a40576d-e284-4df4-bc2a-d9b5cb4577a5n%40googlegroups.com.

[Cecília Álvares]

thanks! ^^