[gmx-developers] pbc and virial problem

[Alexander Herz]

Hey,

indeed it seems very strange, that's why I'm asking :) I cannot see how
a force in z only can affect average atom x/y positions in a periodic
system.
You understand correctly, the only things I write to are (just like the
walls code):

f[i][ZZ]
Vtot

which causes the long term average of fshift[XX][XX], fshift[YY][YY]
(and possibly others but not fshift [ZZ][ZZ]) to
change by about 300. The local virial contribution long term average is
not affected (so the virial from the home atoms without shift).
I do include the virial correction to avoid the assymetry (this is how I
detected that problem).

I'll try to calc the shifted virial contribution twice, once with and
once without the correction
inside mdrun and compare the results.

Alex

hessb at mpip-mainz.mpg.de schrieb:
> Hi,
>
> What you are saying seems a bit contradictory.
> Do I understand it correctly that you only add something
> to the z component of the force (and not to the shift force)
> and then the components of the shift forces change, which
> affect only the xx and yy components of the virial?
> That seems very strange.
> This almost must mean that somehow the position of atoms
> along x and y changes due to your extra force.
>
> For your force you have taken care of the correction that was missing
> in the wall potentials that caused the asymmetry?
>
> Berk
>
>   
>> Hi,
>>
>> I've added a force similar to the walls. Now I'm trying to calculate
>> surface tensions using this new correction via the virial.
>> We used to do these calculations with pbc=xyz with an older gromacs
>> version so I'm trying to do the same in order to be able compare the
>> results before going to pbc=xy.
>>
>> The problem is that I get non sense for the virial xx and yy components.
>> To figure out why, I compared the averaged virials for the same sim with
>> and without the new correction.
>>
>> The virial contribution from the non-shifted particles is pretty much
>> identical but the virial from the shifted
>> particles:
>>   (calc_virial in sim_util.c):
>>   clear_mat(vir_part);
>>
>> calc_vir(fplog,SHIFTS,fr->shift_vec,fr->fshift,vir_part,ePBC==epbcSCREW,box);
>>   inc_nrnb(nrnb,eNR_VIRIAL,SHIFTS);
>>
>> differs by almost exactly the amount which I'd expect.
>>
>> The correction I apply only adds forces in z direction and the
>> simulation is setup such that no pbc in z is applied because of the cut
>> off (there is a water slab of ca. 6 nm thickness in the middle of the
>> box (z direction) surrounded by ca. 3 nm of nothing in both z
>> directions). Debugging through the code I can see that no images for
>> z!=0 are created.
>> The correction force is quite small compared to the forces applied by
>> gromacs non_bonded
>> (correction: avrg. force=0.03, max. force=8.0, gromacs: avrg.:456.0 ,
>> max.: 4831.0).
>>
>> The force is calculated just after the walls right before do_nonbonded.
>>
>> Finally, the question:
>> Any ideas how the small additional force in z direction can have such a
>> strong effect on the virial xx and yy components
>> (apparently fshifted[XX] and fshifted[YY] are influenced significantly
>> whereas the virial ZZ value remains virtually identical
>> no matter if the correction is applied or not, as fshifted[ZZ]==0 in
>> both cases).
>>
>> Thx,
>> Alex
>>
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