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Joined: Jul 2004
Posts: 32
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Joined: Jul 2004
Posts: 32
Hi, all,

I have noted that the energy terms for CONS RMSD and CONS HARM BESTFIT are neglected in PERT! I am using version c43b2.

Example CHARMM code:

cons rmsd force 20.0 sele segid HETA .and. .not. hydrogen end
energy
pert
energy lambda 0.0 lstart 0.0 lstop 0.0
energy lambda 1.0 lstart 1.0 lstop 1.0

yields as energies:

BEFORE PERT

ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER CONSTR: HARMonic CDIHedral CIC RESDistance NOE
ENER> 0-180767.16559 -38473.33688 12.96067
ENER INTERN> 364.99972 855.92916 105.91482 1090.40004 65.60894
ENER CROSS> -40.40268 0.00000 0.00000 0.00000
ENER EXTERN> 20193.60282-203406.86527 0.00000 0.00000 0.00000
ENER CONSTR> 3.64685 0.00000 0.00000 0.00000 0.00000

AFTER PERT (lambda=0.0)
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER> 0-180770.81244 3.64685 12.96067
ENER INTERN> 364.99972 855.92916 105.91482 1090.40004 65.60894
ENER CROSS> -40.40268 0.00000 0.00000 0.00000
ENER EXTERN> 20193.60282-203406.86527 0.00000 0.00000 0.00000

AFTER PERT (lambda=1.0)
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER> 0-180770.81244 3.64685 12.96067
ENER INTERN> 364.99972 855.92916 105.91482 1090.40004 65.60894
ENER CROSS> -40.40268 0.00000 0.00000 0.00000
ENER EXTERN> 20193.60282-203406.86527 0.00000 0.00000 0.00000


As you can see the entry for "CONS RMSD" disappeared after PERT initiation. The total energy differs by 3.65 kcal/mol (which is the restraining potential energy).
The same is true if PERT qmmm is used. Interestingly, the CONS HARM command (without BESTFIT) is ported to PERT.

Any idea how one can used RMSD restraints with PERT?

Thanks for any insights!
Best,
Martin

Joined: Jul 2004
Posts: 32
Forum Member
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Joined: Jul 2004
Posts: 32
To be more precis, I am not interested in "mutating" the CONS RMSD term with PERT. I just want to keep a constant RMSD restraint on my HETA heavy atoms during the PERT simulations.


Moderated by  BRBrooks, lennart, rmv 

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