From: Hadi (dinpajooh_at_gmail.com)
Date: Fri Aug 02 2013 - 13:28:46 CDT
Thanks for your note!
I am not sure what project Frank is working on. As you may notice, if one
develops a new forcefield (not necessarily CHARMM FF), similar to my
project, they may choose different reasonable force constants, etc.
On Fri, Aug 2, 2013 at 9:01 AM, Kenno Vanommeslaeghe <
> Hi Frank and Hadi,
> I just had a talk with the lead developer of the CHARMM Drude polarizable
> force field to settle this.
> On 08/01/2013 07:48 AM, Frank Haverkort wrote:
>> In the PSF file, the drude charge q_D and the polarizability alpha are
>> specified. On the other hand, the force constant for the drude particle
>> k_D is specified in the force field parameter file. But since these
>> quantities are related via alpha = q_D^2 / k_D, why is it not sufficient
>> to define only two of them in the input files? Now it seems that I
>> manually have to calculate the force constant k_D from a given alpha and
> The force constant from the parameter file is used, and is currently the
> same for all Drude particles. When CHARMM builds an XPLOR psf based on the
> CHARMM topology file, it uses the alpha to determine the *charge* on the
> drude particle. So it would indeed appear that having both the charge and
> the alpha in the psf would be redundant. Probably it's just the format
> specifications. Perhaps the more important question is which of the two
> NAMD actually uses. If I were to make a guess, I would say the charge, but
> maybe a NAMD developer can answer that question for sure.
> This statement seems to contradict the statement I found on this mailing
>> list, that the Drude force constants are specified in the force field
>> parameter file.
> The force constants *are* specified in the parameter file, but in the
> CHARMM Drude polarizable FF, we happen to constrain ourselves to using just
> one force constant for all Drude particles.
> On 08/01/2013 02:39 PM, Hadi Dinpajooh wrote:
>> The PSF file contains information about q_D, polarizability (alpha),
>> lone-pairs, thole parameter, etc., but it does not contain any information
>> about force constant. You should add force constant information to the
>> parameter file when you run NAMD simulations.
> If we're talking about the CHARMM Drude polarizable FF, all necessary the
> force constant information is already in the parameter file in the from of
> a wildcard:
> X DRUD 500.00 0.000
> Versions of NAMD that are new enough to run Drude simulations correctly do
> recognize this syntax.
> You do need to calculate the
>> force constant, k_D, for given values of alpha and q_D.
> Nope, the second option is the correct one:
> However, you can
>> calculate q_D for given values of alpha and k_D instead (I believe this is
>> how CHARMM generates PSF files).
> If you use a very stiff force constant,
>> then the displacement of the Drude particle remains much smaller than any
>> interatomic distance. Also note that if you want to use a force constant
>> of 1000 kcal/(mol Ang^2), you should set it to 500 kcal/(mol Ang^2) in the
>> parameter file due to the potential function used for bond stretches, i.e.
>> V(bond) = Kb(b - b0)**2.
> You should use the force constant that came with the force field. Choosing
> something else may lead to problems.
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