Ok. Thanks I will see if I get an answer from someone else.
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 - 20:00:03 PDT
