Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run

From: Peter Freddolino (
Date: Mon Nov 10 2008 - 20:02:10 CST

You should, I'll note, expect your protein to drift a bit given that it
should still diffuse...

Mamta Mohan wrote:
> Dear Peter,
> Thank you for the explanation.
> I think same will be true for protein drift too.
> I will try what you suggest and write to you if I still have doubts.
> Thank you.
> Mamta Mohan
> ----- Original Message ----- From: "Peter Freddolino"
> <>
> To: "Mamta Mohan" <>
> Cc: <>; <>
> Sent: Monday, November 10, 2008 2:52 PM
> Subject: Re: namd-l: Simulation issues: water box deformation after
> minimization and shifting protein coordinates during production run
>> Mamta Mohan wrote:
>>> Dear Peter,
>>> Perhaps I missed some explanation in the previous mail.
>>> The periodic cell I defined I used minmax and listed the coordinates
>>> (I can list the macro if you want). The coordinates of the box are not
>>> touched once box was built. The box itself seems to have shifted after
>>> minimization. In the snapshot I redraw to box to explain my point.
>> My point is that measuring the minimum and maximum coordinates in vmd is
>> meaningless if some components of the system are not wrapped, and that
>> the reason that your water box appears to "jump" is that you *are*
>> wrapping the water coordinates into a box with a different center from
>> the start of the simulation (unless I misread your original email, which
>> seems to indicate that your pre-simulation box is centered near
>> (0,0,0)). Rather than measuring the system minmax in vmd to figure out
>> how big the actual periodic box is after the simulation, look at the box
>> size and center in the .xst file from namd. The box you've drawn in your
>> snapshots is meaningless because you're not measuring it based on what
>> the actual periodic cell is.
>> Try drawing the box present in your .xst file before, during, and after
>> the simulation.
>>> Minimization and production ran as one step (please take a look at
>>> config file)
>>> The snapshots I took by superimposing the two molecules (as explained
>>> below in the mail) to make my point. First molecule is before
>>> minimization and production run, that is psf+pdb and second is after
>>> simulation finished psf+dcd.
>>>> From what I see, water box shifted and protein seems to be drifting
>>> constantly towards the top of the box during production run.
>>> I also think (and please explain me why if I am incorrect) that I do
>>> not have to wrap proteins and ions, I think wrap water should be OK. I
>>> can wrap dcd later for protein and ions.
>> You don't have to; it is fine to wrap whichever system components you
>> want unless you're doing something like a diffusion constant
>> calculation. However, you cannot then trust the results of measure
>> minmax to tell you what your periodic cell size is, because some of the
>> atoms are not *in* the coordinates of the unit cell (indeed, you never
>> can if you have a protein, since its coordinates will not always be
>> contained within the periodic cell).
>> Peter
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