[gmx-developers] tpic with large cavities

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 17 09:13:46 CET 2010

On 2010-11-17 08.12, hess at sbc.su.se wrote:
>> Hi all,
>> Currently I'm looking into the cavity test particle insertion (TPIC) code
>> since I want to make a modified version of the algorithm. Due to obtaining
>> strange results I started to do some testing of the original tpic
>> algorithm (using the current git version). My test system is a plain water
>> box into which I insert a helium atom. I calculate the energy in a
>> spherical cavity at the center of the box and when the radius of insertion
>> (rtpi in the mdp file) is increased I expect the energies to converge
>> towards the energy calculated using the standard TPI algorithm for the
>> whole box.
>> Small radii gives quite accurate energies, but large radii give much lower
>> energies than expected. A clue might be that the threshold for my system
>> lies around the size of the cutoff. When I tried to debug the code I
>> noticed that (as far as I can see) do_forces are using the center of the
>> cavity instead of the actual insertion point. But setting
>> "fr->cg_cm[top->cgs.nr-1]" to "x_tp" instead of "x_init" did not help.
>> This should not be a sampling problem since insufficient sampling would
>> overestimate the energy rather than underestimate it. (And the energies
>> seems to converge nicely too.)
> I guess your problem problem is that r_tpi is large compared to rlist.
> As the manual says, neighbor searching is done only once per step.
> The neighborlist is made with respect to the center of the cavity,
> but the energies are determined for the actual location of the molecule.
So this means the algorithm can only be used in practice for very small 
>> Another problem in the TPIC code is that the box volume is used to
>> calculate the energies instead of the volume of the insertion sphere
>> (which is constant and cancels out in the equation). This might give large
>> errors if the box volume changes a lot due to pressure rescaling.
> The volume issue is always tricky.
> This corrects for the probability of encountering the certain part
> of space where you are inserting. We should not correct for the volume
> of the whole box. But I don't see immediately if and if so,
> what type of volume correction is required for tpic.
> Berk
>> Ideas and comments are most welcome!
>> Best regards,
>> Daniel
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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

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