Re: pKa calculation with thermodynamic integration (TI)

From: Brian Radak (bradak_at_anl.gov)
Date: Tue May 23 2017 - 09:32:14 CDT

Those are defined in the parameter file that I sent
(par_cph36_prot.prm). In principle, many of those parameters do not
affect the final value, but DO affect the rate of convergence. Just to
be clear, I cannot, at this time, offer any guarantees on the latter -
they are experimental.

The only important thing is that the dummy atoms:
1) do not have Lennard-Jones interactions with other particles
2) only have minimal bonded interactions with the rest of the system

Both of those requirements are met by the parameters I defined.

Cheers,
Brian

On 05/23/2017 01:04 AM, Sadegh Faramarzi Ganjabad wrote:
> Brian,
>
> I already used "set beta" keyword of VMD to assign values for beta.
> Now I'm wondering about parameters for dummy atoms. NAMD complains
> about not finding vdw parameter for HD atom type, for example. Do I
> have to manually assign a value (say 0) for that?
>
> Thanks,
> Sadegh
>
> On Wed, May 17, 2017 at 10:54 AM, Radak, Brian K <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> wrote:
>
> You can do all of this from inside psfgen now:
>
> patch GLUHD <segid:resid>
> regenerate angles dihedrals
> guesscoord
>
> set atom0List {CG HG1 HG2 CD OE1 HE1 OE2 HE2}
> foreach atom0 $atom0List {
> set atom1 [format "%d1" $atom0] ; # this only works bc of the
> arbitrary naming convention in the patch
> psfset beta $atom0 -1.0
> psfset beta $atom1 1.0
> }
>
> writepsf <psfname>
> writepdb <pdbname> ;# this assigns atom indices to all of the atoms
>
> set ebondsfile [open "foo.extrabonds" "w"]
> foreach atom0 $atom0List {
> set atom1 [format "%d1" $atom0] ;
> set i [expr {segment atomid <segid> <resid> $atom0] - 1}] ;#
> note the index shift
> set j [expr {segment atomid <segid> <resid> $atom1] - 1}]
> puts $ebondsfile [format "bond %d %d %f %f" $i $j 100.0 0.0]
> }
> close $ebondsfile
>
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643 <tel:%28630%29%20252-8643>
> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> [owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>] on
> behalf of Hannes Loeffler [Hannes.Loeffler_at_stfc.ac.uk
> <mailto:Hannes.Loeffler_at_stfc.ac.uk>]
> Sent: Wednesday, May 17, 2017 3:37 AM
> To: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>; Sadegh
> Faramarzi Ganjabad
> Subject: Re: namd-l: pKa calculation with thermodynamic
> integration (TI)
>
> > Is that what I am supposed to do? if so, how can I tight (for
> > example) CD and CD1 atoms together by a harmonic restraint? at the
> > beginning, there is no distance between them.
>
> You need to mark the outgoing group with -1 in the column that you
> have
> chosen (alchCol). Look into the extraBonds feature to set additional
> restraints.
>
>
> Cheers,
> Hannes.
>
>

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov

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