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#37467 - 04/12/19 08:45 AM Langevin thermostat
pmj Offline
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Registered: 01/15/19
Posts: 30
Dear all,

I would like to use Langevin thermostat in my simulations with implicit solvent. I got confused while reading the posts because most people use the term Lagevin dynamics and Langevin thermostat interchangeably. Can someone one explain why is that so?

Also, since I do not want to use CPT with implicit solvent what would be the keywords I should add to my script to use Langevin thermostat? At which point should I introduce it, immediately after the heating or for example after the heating and 50-100 ps of equilibration?

Thank you so much for your help.

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#37468 - 04/12/19 11:43 AM Re: Langevin thermostat [Re: pmj]
rmv Online   content

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Registered: 09/17/03
Posts: 8323
Loc: 39 03 48 N, 77 06 54 W
A Langevin thermostat is typically Langevin dynamics using a low value of the collision frequency, in order to avoid damping the atomic motions. It works reasonably well for ensemble sampling, but is not suitable for computing time-based properties, as the velocities are perturbed by the random forces. Calculated properties such as molecular diffusion will depend too much on the value of the collision frequency used.

In CHARMM, the setup is something like

! collision freq 1/ps
SCALAR FBETA SET 1.0
DYNA LEAP LANG ...


Switching right after heating should be fine.
_________________________
Rick Venable
computational chemist


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#37470 - 04/17/19 11:28 AM Re: Langevin thermostat [Re: rmv]
pmj Offline
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Registered: 01/15/19
Posts: 30
Dear prof. Venable,

thank you so much for you answer. Do you perhaps know if it is mandatory to use the same collision factor if equilibration and dynamics were done using LD and then afterwards SGLD simulation was done with FBETA 1.0 or 2.0?

Thank you

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#37471 - 04/17/19 12:56 PM Re: Langevin thermostat [Re: pmj]
rmv Online   content

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Registered: 09/17/03
Posts: 8323
Loc: 39 03 48 N, 77 06 54 W
It doesn't much matter; the change from LD to SGLD is itself significant, and they should be regarded as two separate simulations.
_________________________
Rick Venable
computational chemist


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#37472 - Today at 06:20 AM Re: Langevin thermostat [Re: rmv]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 30
Dear prof. Venable,

I see, thank you for all your answers.

Also, I wanted to know whether I should use parameters/topology with CMAP for proteins if I also have nucleic acids in my system, since CMAP term is added only to the proteins?

Thank you

All best

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#37473 - Today at 10:46 AM Re: Langevin thermostat [Re: pmj]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8323
Loc: 39 03 48 N, 77 06 54 W
The force field files are modular, in that you don't need the "prot" files if your system does not contain any amino acids, peptides, or proteins.
_________________________
Rick Venable
computational chemist


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