VMD-L Mailing List

From: Bjørnar Jensen (bje076_at_ift.uib.no)
Date: Mon Jan 14 2013 - 01:53:38 CST

Hi,

there is a "charge" field assigned to each atom that can be accessed
through selections. PME Electrostatics
and volmap tool relies on the value in this field. You can write a
script to manually read and assign the charges.
It's not particularly complicated.

If your charges change from one frame to another, this will complicate
things a bit, at least make
such a solution slower.

PDB files does have a charge field, but if I recall correctly it only
holds integers. I've previously used
the "occupancy" field in the pdb files to have charges assigned to
molecules, but this will not work
when using PME Electrostatics or the Volmap tool. There may be other
file formats that have a suitable
charge field which VMD will read.

I don't think the charge field is unique for each frame, but you'll have
to look this up.

Most workarounds will require some TCL scripting.

Best regards,
Bjørnar.

On 2013-01-11 22:28, mpincu wrote:
> Hello,
>
> I have a trajectory (*.xyz) file, with an additional field after the
> coordinates that contains the Mulliken charge of the atom. My system
> is a charged molecule (gas phase simulation). I was wondering if
> there is any tool to create a representation of the dynamic charge
> distribution along the trajectory ?
> I did look briefly at PME electrostatics extension, but I don't really
> understand what kind of input it expects; clearly it does not
> understand to read the charge from the xyz file.
> Can anyone suggest a workaround ? For example, can I transform my
> input file or perhaps I should create a charge input file ? What type
> of inputs does PME Electrostatics expect.
> Thanks,
>
> Madeleine