Re: Harmonic Constraint: 2 types

From: Morad Alawneh (
Date: Thu Nov 30 2006 - 14:32:27 CST

Thank you for your suggestion.

Unfortunately, as you said it works with center of mass only, and that is not sufficient for me.
I would like to apply a planer harmonic constraint on each P atom of the lipid head group, Do you have any other suggestions?


Morad Alawneh

JC Gumbart wrote:
SMD can be used to apply a constraint along one axis only.  So you could use SMD for the lipid headgroups with a velocity of 0 and a direction of 0 0 1.  It only applies to the center of mass actually, but hopefully this will be sufficient for your purposes.  Then you can just use harmonic constraints for your protein.

On Nov 26, 2006, at 7:36 PM, Morad Alawneh wrote:

Dear NAMD users,

I would like to have two kinds of harmonic constraints in my system.
The first one is constraining the protein harmonically in the x, y, and z directions.
The second one is constraining the lipids' headgroup in the z direction (PLANER CONSTRAINT).

According to what I read in the manual, only one kind can be applied.

Does any one have an idea how to do that?

Thank you.

Morad Alawneh

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