[gmx-developers] virial symmetry

[Berk Hess]

Ah, thanks!

That is indeed incorrect.
The same correction should also be applied for x and y on the lower wall.

But it is not really Newton's 3rd law here, but the Gromacs single sum 
virial trick.

PS in your last line [XX][XX] should be [XX][ZZ]
(but I should check the order of the two components in the virial).

Berk

Alexander Herz wrote:
> Hi,
>
> no I haven't changed the walls.
>
> the virial contains : r_x*F_z, r_y*F_z and r_z*F_z in components other
> then [ZZ][ZZ]
> But the only correction made to the virial for the walls is for the
> zz,zz component (last line of the wall code you copied)!
> So (unlike for the rest of the pair potentials like lennard jones,
> estat, etc.) the wall contribution to the virial via the atom forces is
> position dependent!
>
> To reproduce the problem:
> make a small sim with 2 walls which are identical except density (make
> em differ by a factor of 10 or so)
> and then look at the average virial at the end of the md.log, it will be
> asymmetric (so theta_ij!=theta_ji).
>
> to fix the problem I'd suggest:
>
> inside the force calculating loop:
> instead of
>
> Fwall[w]+=(-F);
>
> do:
> //force MUST act on the same x/y coord as the particle otherwise newtons
> 3rd law is violated
> fr->vir_wall[XX]+=-0.5*x[i][XX]*(-F);
> fr->vir_wall[YY]+=-0.5*x[i][YY]*(-F);
> fr->vir_wall[XX]+=-0.5*box_zz*(-F);
>
> and inside sim_util.c:
>
> vir_part[XX][XX]+=fr->vir_wall[XX];
> vir_part[YY][ZZ]+=fr->vir_wall[YY];
> vir_part[ZZ][ZZ]+=fr->vir_wall[ZZ];
>
> Alex
>
>
> Berk Hess wrote:
>   
>> Hi,
>>
>> At the end of do_walls it says:
>>
>>  /* Since the lower wall is at z=0 it does not contribute
>>   * to the single sum virial.
>>   */
>>  if (nwall == 2)
>>    fr->vir_wall_zz = -0.5*box_zz*Fwall[1];
>>
>> This line should ensure that the virial only depends on the distance
>> between the particles and the upper wall.
>>
>> I don't understand what you mean with asymmetric.
>> The wall only acts on the z-component of the forces and both the force
>> and distance have no x and y
>> components, therefore the wall forces only occur in the zz element of
>> the virial tensor.
>>
>> Have you modified the code such that this correction no longer holds?
>>
>> Berk
>>
>> Alexander Herz wrote:
>>     
>>> Having looked a bit closer into this, it seams that the definition of
>>> the virial used in gromacs
>>> (using absolute particle coords) is obviously only translation invariant
>>> as long newtons 3rd law
>>> is obeyed inside the system and no external forces act on the system (so
>>> all forces sum to zero).
>>> Apparently this condition is violated when using 2 walls with different
>>> parameters like density???
>>>
>>> Alex
>>>
>>> Alexander Herz wrote:
>>>  
>>>       
>>>> Hi guys,
>>>>
>>>> I'm having some problems with the walls feature (new in gromacs 4.0).
>>>>
>>>> If I understand correctly then I do get a symmetric virial tensor
>>>> even for
>>>> systems which are inhomogenous as long only pair potentials are used
>>>>
>>>> (Theta=-0.5*sum(r_ij*F_ij) where r_ij is r_j-r_i (so the distance
>>>> between to particles acting on each other)
>>>> and F_ij is the force acting on them;with F_ij=-F_ji the contributions
>>>> cancel out and the viral is symmetric )
>>>>
>>>> Now if I use 2 walls with different density I get an asymmetric virial
>>>> and looking at the wall's source
>>>> it seams that for walls not r_ij is used but absolute wall coordinate
>>>> (box_zz for wall2 and 0 for wall 1
>>>> giving a zero contribution to the viral for wall1). Also for the
>>>> individual atoms it seams the absolute position
>>>> is used rather than r_ij (looking at calc_vir() in calcvir.c).
>>>>
>>>> So why do the walls use the absolute z coordinate instead of
>>>> particle_z-wall_z and why
>>>> do I get an asymmetric virial for walls with different density but not
>>>> for the same
>>>> system without walls which is still asymmetric in z (some crystal
>>>> occupies the lower z half off the system, the upper
>>>> half is filled with water).
>>>>
>>>> Thx,
>>>> Alex
>>>>
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