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#37467 - 04/12/19 08:45 AM Langevin thermostat
pmj Offline
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Registered: 01/15/19
Posts: 44
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
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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: 44
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: 8364
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 - 04/24/19 06:20 AM Re: Langevin thermostat [Re: rmv]
pmj Offline
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Registered: 01/15/19
Posts: 44
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 - 04/24/19 10:46 AM Re: Langevin thermostat [Re: pmj]
rmv Online   content

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Registered: 09/17/03
Posts: 8364
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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#37474 - 04/24/19 03:46 PM Re: Langevin thermostat [Re: pmj]
lennart Online   content

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The CHARMM additive forcefield (current version 36) is really just ONE forcefield, which for practical reasons is contained in a small set of component files, which are all fully compatible with each other. You simply read the files that your application requires - if you are unsure you could read them all.

Similarly the polarizable version is ONE forcefield, with a number of mutually compatible components.

So, yes, you can (and should) read the potein and nucleic acid files AS THEY ARE.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37476 - 04/25/19 02:59 AM Re: Langevin thermostat [Re: pmj]
pmj Offline
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Registered: 01/15/19
Posts: 44
Dear prof. Venable and Nilsson,

thank you for your answers. I am using both files as they are, but I just wanted to check.

Also, regarding the Langevin thermostat/dynamics. Since in the examples and recommended scripts in the documentation there is only one file for heating, equilibration and analysis runs, I was just wondering where is the limit of each phase? After certain amount of time, am I supposed to switch to normal dynamics or proceed with LD?

Do you have some suggestions on how to properly equilibrate system with RNA?

Thank you

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#37479 - 04/25/19 11:12 AM Re: Langevin thermostat [Re: pmj]
rmv Online   content

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Registered: 09/17/03
Posts: 8364
Loc: 39 03 48 N, 77 06 54 W
There is not a hard rule about how much time to spend on each phase, but I've found that by starting at ca. 200 K, heating and initial thermal equilibration can usually be accomplished in about a nanosecond. (Note that Langevin should NOT be used during heating.)

General system equilibration is not so easily defined; I generally monitor time series for a number of properties such as potential energy, radius of gyration, backbone dihedrals, etc., to look for evidence that a steady state has been achieved, which can easily take a hundred or hundreds of nanoseconds. The details of the specific system are a major factor, with larger and more complex systems requiring longer equilibration times.
_________________________
Rick Venable
computational chemist


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#37482 - 04/29/19 10:02 AM Re: Langevin thermostat [Re: rmv]
pmj Offline
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Registered: 01/15/19
Posts: 44
Dear prof. Venable,

thank you for all advices.

One more thing, in the documentation the following was written for LD simulations:

3) For heating, equilibration and analysis runs using

Langevin dynamics:(+)

DYNA LEAP LANGEVIN STRT(*) NSTEP 20000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 - ILBFRQ 1000 RBUFFER 0.0 TBATH 300.0 - hbond-spec nonbond-spec - FIRSTT 300.0 FINALT 300.0 - IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

(+) Note that the friction coefficients, in units of 1/ps, must first be initialized by filling the array FBETA with the SCALAR command SCALAR FBETA SET (*)
Except for first run, the use STRT in place of RESTART

I do not understand how one can know at which point equilibration phase is done, and production phase starts since it is only one script for both?

All best

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