[gmx-users] potential energy of a peptide in explicit DMSO
Xiaoming Zhang
smash04 at gmail.com
Fri Jul 29 04:18:47 CEST 2005
Yes, it is working! Thanks.
I set those force constants to zero in dmso.itp and then rerun the md
simulation. The bonded energies seem reasonable. After adding bonded
and non-bonding energies all together, I got a positive potential
energy (~700 kJ/mol) for peptide alone. Is it normal to see the
positive pot.E in gromacs?
I also have another question regarding the conformational transition
during the md simulation. I observed two major clusters of
conformers during a 100ns simulation, cluster 1 has population ~80%
and cluster 2 has ~15%. I assume that the average potential energy of
cluster 1 should be lower than cluster 2. However, the calculated
average potential energy of cluster 1 is ~10kJ/mole higher than that
of cluster 2. Does that mean I did the energy calculation
incorrectly?
Thanks in advance for your help,
xm
On 7/27/05, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-07-27 at 13:18 -0500, Xiaoming Zhang wrote:
> > Thank you, David. My solvent is DMSO. I guess it will make
> > contribution to bondeds? If it does, then seems difficult to isolate
> > the bonded energies for the peptide.
> Yes. You could do it using -rerun and setting all the force constants
> for DMSO to zero.
>
> >
> > xm
> >
> > On 7/27/05, David <spoel at xray.bmc.uu.se> wrote:
> > > On Tue, 2005-07-26 at 22:14 -0500, Xiaoming Zhang wrote:
> > > > Sorry, I should also include the bonded terms. But those bondeds are
> > > > for the whole system, aren't they?
> > > yes, but if the rest is water there is no contribution to the bonded
> > > energy.
> > > > xm
> > > >
> > > > On 7/26/05, Xiaoming Zhang <smash04 at gmail.com> wrote:
> > > > > Thanks a lot, Anton. I simply changed the energy group in .mdp file
> > > > > from "System" to "Protein" and then I can see some energy terms for
> > > > > the protein when using g_energy. However, I am confused about which
> > > > > energy terms I should used to calculate the potential energy for the
> > > > > peptide. I searched the gromacs achieve and noticed that some other
> > > > > users had the same confusion but no clear answer had been provided.
> > > > > The following is my energy output from g_energy:
> > > > >
> > > > > **************************************************************************************
> > > > > Select the terms you want from the following list
> > > > > End your selection with 0
> > > > > 1= Bond 2= Angle 3= Proper Dih. 4=Ryckaert-Bell.
> > > > > 5= Improper Dih. 6= LJ-14 7= Coulomb-14 8= LJ (SR)
> > > > > 9= Disper. corr. 10= Coulomb (SR) 11= Coulomb (LR) 12= Potential
> > > > > 13= Kinetic En. 14= Total Energy 15= Temperature 16=Pressure (bar)
> > > > > 17= Box-X 18= Box-Y 19= Box-Z 20= Volume
> > > > > 21= Density (SI) 22= pV 23= Vir-XX 24= Vir-XY
> > > > > 25= Vir-XZ 26= Vir-YX 27= Vir-YY 28= Vir-YZ
> > > > > 29= Vir-ZX 30= Vir-ZY 31= Vir-ZZ 32= Pres-XX (bar)
> > > > > 33= Pres-XY (bar) 34= Pres-XZ (bar) 35= Pres-YX (bar) 36= Pres-YY (bar)
> > > > > 37= Pres-YZ (bar) 38= Pres-ZX (bar) 39= Pres-ZY (bar) 40= Pres-ZZ (bar)
> > > > > 41= #Surf*SurfTen 42= Pcoupl-Mu-XX 43= Pcoupl-Mu-YY 44= Pcoupl-Mu-ZZ
> > > > > 45= Mu-X 46= Mu-Y 47= Mu-Z
> > > > > 48=Coul-SR:Protein-Protein
> > > > > 49=LJ:Protein-Protein 50=Coul-LR:Protein-Protein
> > > > > 51=Coul-14:Protein-Protein 52=LJ-14:Protein-Protein
> > > > > 53=Coul-SR:Protein-rest 54=LJ:Protein-rest 55=Coul-LR:Protein-rest
> > > > > 56=Coul-14:Protein-rest
> > > > > 57=LJ-14:Protein-rest 58=Coul-SR:rest-rest 59= LJ:rest-rest
> > > > > 60=Coul-LR:rest-rest
> > > > > 61=Coul-14:rest-rest 62=LJ-14:rest-rest 63= T-System 64= Lamb-System
> > > > > 48
> > > > > 49
> > > > > 50
> > > > > 51
> > > > > 52
> > > > > 0
> > > > >
> > > > > Back Off! I just backed up energy.xvg to ./#energy.xvg.4#
> > > > > Reading frame 70 time 35.000
> > > > > Last frame read 76
> > > > > WARNING: Incomplete frame: nr 77 time 38.000
> > > > >
> > > > >
> > > > > Statistics over 37501 steps [ 0.0000 thru 37.5000 ps ], 5 data sets
> > > > >
> > > > > Energy Average RMSD Fluct. Drift Tot-Drift
> > > > > -------------------------------------------------------------------------------
> > > > > Coul-SR:Protein-Protein -345.062 13.3941 12.7896 -0.367516 -13.7822
> > > > > LJ:Protein-Protein -33.7676 7.30473 7.02883 -0.183696 -6.88877
> > > > > Coul-LR:Protein-Protein 0 0 0 0 0
> > > > > Coul-14:Protein-Protein 719.375 9.16447 8.66907 0.274566 10.2965
> > > > > LJ-14:Protein-Protein 71.2596 9.28124 9.27777 -0.0234419 -0.879095
> > > > >
> > > > > gcq#225: "Everybody is Smashing Things Down" (Offspring)
> > > > >
> > > > > ****************************************************************************************
> > > > >
> > > > > Is it correct to simply add up those five energies to get potential energy?
> > > > >
> > > > >
> > > > > thanks,
> > > > > xm
> > > > >
> > > > >
> > > > >
> > > > > On 7/26/05, Anton Feenstra <feenstra at few.vu.nl> wrote:
> > > > > > Xiaoming Zhang wrote:
> > > > > >
> > > > > > > Dear users,
> > > > > > >
> > > > > > > I am running the MD simulation of a cyclic peptide in explicit DMSO.
> > > > > > > It is straightforward to retrieve the potential energy of the whole
> > > > > > > system (peptide + DMSO) using g_energy. However, I didn't find a way
> > > > > > > to calculate/retrieve the potential energy for the peptide only. I
> > > > > > > was wondering if any of you had the experience and knew how to deal
> > > > > > > with it.
> > > > > >
> > > > > > You need to define energy groups in your mdp file before you perform the
> > > > > > simulation. Alternately, you can re-run your generated trajectory. See
> > > > > > manual for more details.
> > > > > >
> > > > > > --
> > > > > > Groetjes,
> > > > > >
> > > > > > Anton
> > > > > >
> > > > > > * NOTE: New Phone & Fax numbers (below) *
> > > > > >
> > > > > > _____________ _______________________________________________________
> > > > > > | | |
> > > > > > | _ _ ___,| K. Anton Feenstra |
> > > > > > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > > > > > |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> > > > > > | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
> > > > > > | | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
> > > > > > | | "If You See Me Getting High, Knock Me Down" (RHCP) |
> > > > > > |_____________|_______________________________________________________|
> > > > > >
> > > > >
> > > > _______________________________________________
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> > > --
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> > >
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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