**From:** Sadegh Faramarzi Ganjabad (*safaramarziganjabad_at_mix.wvu.edu*)

**Date:** Mon May 08 2017 - 14:59:06 CDT

**Next message:**Vermaas, Joshua: "Re: pKa calculation with thermodynamic integration (TI)"**Previous message:**Eric Smoll: "Question about new NAMD QM/MM code"**Next in thread:**Vermaas, Joshua: "Re: pKa calculation with thermodynamic integration (TI)"**Reply:**Vermaas, Joshua: "Re: pKa calculation with thermodynamic integration (TI)"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear all,

I am planning to calculate pKa of a Glu in a membrane protein with

thermodynamic integration method. As you know, CHARMM 36 has parameters for

both protonated and deprotonated Glu. However, there is no NAMD tutorial on

TI. I had few questions about my system setup. I assume that the dual

topology should be the same as free energy perturbation (FEP). And the

following terminal group of Glu needs to be changed during the perturbation

process

GROUP

ATOM CG CT2 -0.21 !

ATOM HG1 HA2 0.09 ! HG1 OE1

ATOM HG2 HA2 0.09 ! | //

ATOM CD CD 0.75 ! -CG--CD

ATOM OE1 OB -0.55 ! | \

ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2

ATOM HE2 H 0.44 !

BOND OE2 HE2

Then, is this group supposed to vanish during the perturbation and a new

group should appear at the same position, with HE2 omitted and updated

partial charges for the rest of atoms? or only HE2 vanished and the charges

of other atoms are updated without vanishing/appearing? for the latter I am

not sure what the dual topology would look like (with keeping the atoms at

same positions and only reassigning partial charges).

Also, I am not sure what differences would be between FEP and TI in terms

of simulation procedure. I know the theory of each method, but compared to

FEP, there is no clear instructions about running TI as I said. In

'fep.tcl' script of FEP tutorial files there is a section for TI but I

don't know how to use it. Any help is highly appreciated.

Thanks,

Sadegh

**Next message:**Vermaas, Joshua: "Re: pKa calculation with thermodynamic integration (TI)"**Previous message:**Eric Smoll: "Question about new NAMD QM/MM code"**Next in thread:**Vermaas, Joshua: "Re: pKa calculation with thermodynamic integration (TI)"**Reply:**Vermaas, Joshua: "Re: pKa calculation with thermodynamic integration (TI)"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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