Re: Avoiding Rotation and translation of protein

From: Marc Q. Ma (
Date: Wed Jun 08 2005 - 16:58:02 CDT

If the linear momenta are all zero in x, y and z directions, then the
protein should not be translocated if the system is conservative. You
should remove the COM motion of the protein anyway so that you have a
zero momentum to start with.

NPT systems are not conservative. You may try NVE microcanonical
simulations after you use NPT simulation to get the system into an
equilibrated state -- size, density, COM, energy, temperature .... all

Meanwhile, you may increase your water box size just to stay on the
safer side.

Hope this helps.

On Jun 8, 2005, at 1:39 PM, Blake Charlebois wrote:

> The following thread may help:
> There are several related (and possibly more useful) threads. You can
> find
> them with a Google search specifying namd-l as one of the search terms.
> You should read the section of the NAMD manual on wrapping
> coordinates. You
> may find some useful scripts on the VMD site for reversing coordinate
> wrapping in a dcd file.
> Does your protein consistently rotate in the same way? Does it have a
> large
> dipole moment? If so, you may want to increase your box size.
> Blake
> -----Original Message-----
> From: [] On
> Behalf
> Of Leonardo Sepulveda Durán
> Sent: June 8, 2005 11:59 AM
> To:
> Subject: namd-l: Avoiding Rotation and translation of protein
> Hello!!!!!
> I am performing a NPT dynamics of a protein. I use a 10A waterbox, and
> 2 ions (neutral system), PBC and PME. At 400 ps, the protein begins to
> rotate (I dont Know if its center of mass translates too),
> furthermore, one residue comes dangerously close to the border of the
> box. I would like to ask if there is a way to avoid such protein
> movements in the simulation, or whether there is a way to reorganize
> trayectory files later in order to obtain a dcd where this movements
> are taken out. And if that is posible, what happens if one of my
> protein's residue steeps through th boundary? Is that Dynamics lost???
> Thanks

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