Your warming is abrupt, but this should not matter much if
the system is covalently bonded (e.g. unlike nucleic acid
strands).
The energies in molecular mechanics are considered to be
relative. E.g. one can compare the energies of two states
of the same system, but one cannot compare energies of
two different systems. That said, the quantities that attract
my attention are the electrostatic terms, which from my
experience with nucleic acids I somehow expect to be more
negative. This intuition may have no bearing on your system
however.
Hopefully you are visualising the trajectory, which helps
build intuition and understanding.
> In the meantime, I run an implicit solvent minimisation for 500 steps, and
> followed by an MD for 100 ps for equilibration at T=300K. The surprise, is that
> my potential energy is huge (bond and angle terms are soo big)!! I do not know
> why is this.
> This is the beginning of the output, and then some steps later:
> &cntrl
> imin = 0, ntb = 0,
> igb = 1, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 100000, dt = 0.001,
> cut = 12.0
> /
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
> | Flags: MPI
> | New format PARM file being parsed.
> | Version = 1.000 Date = 07/23/10 Time = 02:31:00
> NATOM = 2244 NTYPES = 8 NBONH = 1248 MBONA = 995
> NTHETH = 2930 MTHETA = 1180 NPHIH = 4728 MPHIA = 1377
> NHPARM = 0 NPARM = 0 NNB = 12142 NRES = 121
> NBONA = 995 NTHETA = 1180 NPHIA = 1377 NUMBND = 13
> NUMANG = 28 NPTRA = 7 NATYP = 10 NPHB = 0
> IFBOX = 0 NMXRS = 76 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
> Implicit solvent radii are modified Bondi radii (mbondi)
>
> | Memory Use Allocated
> | Real 123620
> | Hollerith 13587
> | Integer 122970
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 1499 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
> NSTEP = 7400 TIME(PS) = 7.400 TEMP(K) = 291.54 PRESS = 0.0
> Etot = 4154.4925 EKtot = 1950.0576 EPtot = 2204.4348
> BOND = 812.4619 ANGLE = 1818.8081 DIHED = 446.1581
> 1-4 NB = 490.4294 1-4 EEL = -215.7047 VDWAALS = -972.2307
> EELEC = -11.1912 EGB = -164.2959 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
> NSTEP = 7500 TIME(PS) = 7.500 TEMP(K) = 303.29 PRESS = 0.0
> Etot = 4148.7642 EKtot = 2028.6893 EPtot = 2120.0749
> BOND = 782.4092 ANGLE = 1781.6060 DIHED = 450.9169
> 1-4 NB = 472.8182 1-4 EEL = -215.6475 VDWAALS = -980.7847
> EELEC = 2.8606 EGB = -174.1037 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
> NSTEP = 7600 TIME(PS) = 7.600 TEMP(K) = 297.25 PRESS = 0.0
> Etot = 4138.8187 EKtot = 1988.2913 EPtot = 2150.5274
> BOND = 812.9033 ANGLE = 1785.5470 DIHED = 434.3124
> 1-4 NB = 480.2016 1-4 EEL = -220.1416 VDWAALS = -979.8534
> EELEC = 55.0183 EGB = -217.4600 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.EDU>
> To: amber.ambermd.org
> Sent: Sun, July 25, 2010 1:22:44 AM
> Subject: Re: [AMBER] question about bond command
> My apologies, I was thinking of ionic concentrations (which I
> know something about) rather than pH (which I don't).
> Hopefully someone who does know can answer your original
> question.
> Bill
> > Thanks. for this my whole macromolecule is neutral now if i add ions it is
> >going
> >
> > to be charged!! will amber accept calculations with a total charge different
> > from zero? I used addions before in another work when my protein charge was
> > different from zero example addions 8 Na+.
> > In this specific case, there seems to be a need to protonate or something like
> > this for say pH=5. How can I do this since my molecule is already built. And
> >how
> >
> > to know if I am at low pH, or high pH?
> > ________________________________
> > From: Bill Ross <ross.cgl.ucsf.EDU>
> > To: amber.ambermd.org
> > Sent: Sat, July 24, 2010 9:57:32 PM
> > Subject: Re: [AMBER] question about bond command
> > > I want to perform calculations at specific pH. How do I do this in Amber?
> > You must calculate the number of ions to use for the box of water
> > you will create, and add them with leap's addions command after
> > solvation. There is no way to simply request a pH.
> > Bill
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Received on Sat Jul 24 2010 - 20:30:02 PDT
