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

From: Mamta Mohan (
Date: Mon Nov 10 2008 - 14:20:49 CST

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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