[gmx-developers] Scaling velocities in Velocity Verlet

[Shirts, Michael (mrs5pt)]

Hmm.  Which version/branch is this?

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Sat, 3 Dec 2011 22:10:57 +0100
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Scaling velocities in Velocity Verlet
> 
> On 2011-12-03 21:37, Shirts, Michael (mrs5pt) wrote:
>> Hi, all-
>> 
>>> The problem is that the change in Ekin comes one step too late. I tried
>>> to deduce the algorithm from the code (4.5 code base) and deduced the
>>> following MD algorithm:
>> 
>> It's rather difficult to follow currently because of the need to bookkeep
>> both md and md-vv + plus correct pressure control w/constraints. I have high
>> hopes for improving this for 5.0.
>> 
>>> v(t) = v(t-dt/2) + a(t) dt/2
>>> 
>>> v'(t) = lambda v(t)<======= my addition
>>> 
>>> v(t+dt/2) = v'(t) + a(t) dt/2
>>> 
>>> r(t+dt) = r(t) + v(t+dt/2) dt
>>> 
>>> However, the Ekin that is printed is the uncorrected one even though I
>>> scale both ekind->ekin and ekind->tcstat[x].ekinf .
>>> 
>>> Is the algorithm correct as I write it above? Is the Ekin(t) already
>>> stored at the beginning of the time step?
>> 
>> If you add your modification as an option to update_tcouple, and operate on
>> ekind directly (not the velocities), in the same way that berendsen_tcouple
>> does, then the bookkeeping should take care of the velocity rescaling
>> appropriately.
> Close, but no cigar.
> Here's the output from g_energy:
> 
> @ s0 legend "Potential"
> @ s1 legend "Kinetic En."
> @ s2 legend "Total Energy"
>      0.029600  -35405.431557  6460.241804  -28945.189753
>      0.029800  -35407.596247  6462.418642  -28945.177606
>      0.030000  -35327.293038  6466.347370  -28860.945667
>      0.030200  -35330.858001  6387.271571  -28943.586430
>      0.030400  -35334.701690  6391.114750  -28943.586940
> 
> The jump in Potential is at t = 0.03, in Kinetic it is at t = 0.302. As
> you see the Total energy has a peak at t = 0.03, but it does come back
> almost to the right level at the next step. This all makes me think I
> should be scaling the previous velocities, hence my questions about the
> algorithm.
> 
> 
> 
>> 
>> If this _doesn't_ work, then there's some tweaks that got lost in the
>> different versions that are floating around, and I can either put the
>> changes into 4.6 alone, or just add them in with the 4.6 merge.
>> 
>> Best,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821
>> 
>> 
>> 
>>> v(t) = v(t-dt/2) + a(t) dt/2
>>> 
>>> v'(t) = lambda v(t)<======= my addition
>>> 
>>> v(t+dt/2) = v'(t) + a(t) dt/2
>>> 
>>> r(t+dt) = r(t) + v(t+dt/2) dt
>>> 
>>> However, the Ekin that is printed is the uncorrected one even though I
>>> scale both ekind->ekin and ekind->tcstat[x].ekinf .
>>> 
>>> Is the algorithm correct as I write it above? Is the Ekin(t) already
>>> stored at the beginning of the time step?
>>> 
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell&  Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>> --
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-developers-request at gromacs.org.
>> 
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.