From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Sep 14 2018 - 09:37:16 CDT
TL;DR - I'm only responding to the original message.
1) You need to set alchemical partition flags for both particles. By
default these are read from the beta/bfactor column of the PDB file
specified via the "coordinates" keyword. You can automatically set this
from psfgen by using the relatively new "psfset" command. For your example:
psfset beta SOD1 1 SOD 1.0
psfset beta SOD2 1 SOD 1.0
# and then write the pdb via writepdb
2) There really shouldn't be a size effect for a net neutral perturbation,
or at least I am only aware of correction schemes when the net change is to
add or remove charge from the system.
3) You didn't make it clear how you were going to fix the distance between
the particles, but you probably want to use the "extraBonds" command and
add a restraint force. A bond within the PSF should result in electrostatic
and vdW exclusions, which is not what you want. You could also use the
"constraints" command and use a Cartesian reference coordinate set. I'm
also not sure that "fixedAtoms" is a good idea, since it's not always clear
what those constraints are doing when PBCs are in use.
On Fri, Sep 14, 2018 at 8:03 AM Nassar, Omneya <omnassar_at_utmb.edu> wrote:
> Sorry, another mistake: it should be spelled “phosphorus” not
> > On Sep 14, 2018, at 7:47 AM, Nassar, Omneya <omnassar_at_UTMB.EDU> wrote:
> > Hi Ali,
> > I just realized I made a typo and wrote “phosphate” instead of
> “phosphorus” when explaining the elements (Pb for lead and P for
> phosphorus). I accidentally said phosphate because VMD confused the atom
> name “PB” (the beta phosphorous in the phosphate moiety of the nucleotide)
> with the element lead or “Pb”.
> > Thanks again and let me know if you find any misunderstandings or
> conflicting information.
> > Sincerely,
> > Omneya
> >> On Sep 13, 2018, at 9:57 PM, Nassar, Omneya <omnassar_at_UTMB.EDU> wrote:
> >> Dear Ali,
> >> Thank you for your reply and comments. I would like to first apologize
> for all the mistakes I made and for the poor formatting of this email. Here
> are my responses to your comments:
> >> 1. You’re absolutely right. By dipole I didn’t mean dipole moment and
> I meant two oppositely charged point charges (an electric dipole and not a
> permanent dipole).
> >> Response: I’m sorry but I have never heard of an electric dipole and
> permanent dipole. There is only a dipole.
> >> 1. I agree with you that using tcl makes more sense but I was simply
> following NAMD tutorial on FEP calculations and they used pgn extension in
> their alchemical free energy calculation tutorial (Charging a spherical
> >> Response: You are correct. I pulled out my FEP tutorial and did see
> that they used “setup.pgn”. I apologize for the confusion--0000000000004f94f10575d5c311--
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