RE: [NAMD] Apply an electric field only in a specific region

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jun 19 2018 - 08:41:14 CDT

The way I'd interpret the text is that if you don't specify a column to go hunting for "charge", it will use the charge value that NAMD uses for electrostatics (from the psf file if you live in CHARMM-land). If you do specify a column, it will read the value in that column of the fed in pdb as the charge instead.

-Josh

On 2018-06-19 02:48:38-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Thanks for the reply! I've been reading about that function and it does seem to be able to do what I want.
I have one small question, concerning the part where it says:
mgridforcechargecol [$ <$] tag [$ >$] [$ <$] column of PDB from which to read atom charges [$ >$]
Acceptable Values: X, Y, Z, O, or B
Default Value: Atom charge used for electrostatics.
Description: Which column in the PDB file specified by mgridforcefile contains the atom charge. By default, the charge value specified for the short-range Columb interactions are also used for the grid force. Both mgridforcecol and mgridforceqcol can be specified, in which case the apparent charge of the atom will be the product of the two values.

What do they mean with "by default"? If I want to use the charge from the psf files do I just put "1" on whichever column I choose (for example, B)? Or do I have to put those charges in B?
Thanks!!

On Mon, Jun 4, 2018 at 7:33 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
Hi Sebastian, take a look at the mGridForce and related commands.
Giacomo

This archive was generated by hypermail 2.1.6 : Mon Nov 18 2019 - 23:19:53 CST