[gmx-developers] Re: gmx-developers Digest, Vol 16, Issue 12

[Berk Hess]

>  
>
>>I guess there is no conceptual problem and one can always just constrain
>>the full-step velocities. But this does involve coding a velocity
>>version for all constraint algorithms. (I have already implemented LINCS code for this).
>>    
>>
>
>As far as I can tell in the current code, the velocities are simply
>constrained by subtracting the positions.  This is essentially
>equivalent to position verlet -- the coordinates are just the same as
>any other verlet, but the velocities lose some precision,   Can't this
>just be done in velocity verlet as well?  That's also what I've done
>in my version.  I'm not seeing what the problem is here, though I
>admit that these things are -very- subtle, and I could be missing
>something.
>  
>
Subtracting positions leads to the same Ekin problem I have mentioned 
before.
This causes the discretization error in Ekin to be 4 times larger than 
it is now
in the CVS code.

>By the way, there are other, more complicated issues with constraints
>when it comes to pressure control and scaling the system, (which would
>occur with any integration algorithm) as I understand (Michel, you
>could probably explain more!), we should be using the molecular
>virial, as opposed to the atomic virial, and scaling the distance
>between molecular centers, not simply atomic centers.  I'll read up on
>this a little more, but if anybody has looked into this issue more
>carefully, let me know :)
>
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I don't think this is a serious issue.
Atomic virials just cause a bit more noise on the virial.

Berk.