how long you have been running? 20ns? if yes, I suggest to run much longer
like microsecond. For a small peptide, getting this long simulation isn't
difficult. I don't think there is any easy way to tweak the GB parameters
in Amber to make it much more accurate than the current igb8 model. You can
give GBMV in CHARMM a shot but this model is much slower than the ones in
Amber and I am not sure if there is available GPU code for this.
On Tue, Sep 3, 2013 at 4:35 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Hello Hai,
>
> Thanks for your comments. Now the conversation is getting interesting.
>
> I used gbsa=0 with all GB models. I guess that is the less compact it could
> get. At the end of the email is a complete list of parameter values I used.
>
> I didn't do just that simulation. I have done several long aMD simulations
> with igb 8
> along with AMBER12SB or AMBER99SB-NMR1-ILDN of larger ID proteins or
> smaller peptide fragments of them, but all ended up to helical forms. In
> contrast, in TIP4P-Ew + AMBER99SB-NMR1-ILDN aMD runs these
> proteins/peptides remain mostly disordered.
>
> I'd be curious to know if there is any other parameter I could tweak to get
> better results.
>
> best,
> Thomas
>
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
> 10000
> iwrap = 0, ntwx = 1000, ntwv = 0, ntwe
> = 0
> ioutfm = 1, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
> Potential function:
> ntf = 2, ntb = 0, igb = 8, nsnb
> = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
> saltcon = 0.15000, offset = 0.19514, surften = 0.00500
> rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
> alpb = 0
> gbalphaH = 0.78844, gbbetaH = 0.79870, gbgammaH = 0.43733
> gbalphaC = 0.73376, gbbetaC = 0.50638, gbgammaC = 0.20584
> gbalphaN = 0.50336, gbbetaN = 0.31683, gbgammaN = 0.19292
> gbalphaOS = 0.86781, gbbetaOS = 0.87664, gbgammaOS = 0.38788
> gbalphaP = 1.00000, gbbetaP = 0.80000, gbgammaP = 4.85000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Molecular dynamics:
> nstlim = 10000000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = -1.00000
>
> Langevin dynamics temperature regulation:
> ig = 934379
> temp0 = 310.00000, tempi = 100.00000, gamma_ln= 5.00000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00000
>
> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
>
> | Energy averages sample interval:
> | ene_avg_sampling = 100
>
>
>
> On 3 September 2013 22:49, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > In addition, are you using gbsa = 1 or 0? with nonpolar term added, you
> can
> > have more compacted structures.
> >
> >
> > On Tue, Sep 3, 2013 at 3:48 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > On Tue, Sep 3, 2013 at 8:03 AM, Thomas Evangelidis <tevang3.gmail.com
> > >wrote:
> > >
> > >> AMBER12SB. As stated in the AmberTools13 manual (I may have read it
> > >> elsewhere too) that's the only ff that can be used with igb 8.
> > >
> > >
> > > I disagree with this information. Technically, you can use igb=8 with
> any
> > > desired force field. Our work used wildly used ff99SB force field with
> > > igb=8 and got nearly quantitative agreement between simulation and
> > > experiment for our tested small protein (TC5B and HP5F). In the past,
> > > people used a specific combination of force field and solvent model,
> like
> > > ff96 + igb5, to seek for error cancellation. However, this kind of
> > > cancellation should be avoided by using more accurate force field and
> > > solvent model.
> > >
> > > Anyway, how long is your simulation? In our test cases, we also have
> > > quantitative agreement between gb8 and TIP3P data for unstructured
> Ala10
> > > system or helical system like HP1 peptide. For a small system like
> > yours, I
> > > suggest to use REMD to perform extensive sampling since the structure
> > might
> > > stuck in local minimum in microsecond time scale in regular MD
> > simulation.
> > > You can do further by running explicit solvent simulation to compare.
> > >
> > > For igb7, this model just doesn't "like" any folded structure, so you
> > > should expect to get lots of unstructured conformation. However, this
> > does
> > > not mean it will give you the correct answer.
> > >
> > > Hai Nguyen
> > >
> > >
> > >> I also made
> > >> sure to use mbondi3 with igb 8 and bondi with igb 7.
> > >>
> > >>
> > >> On 3 September 2013 14:56, Carlos Simmerling <
> > carlos.simmerling.gmail.com
> > >> >wrote:
> > >>
> > >> > The physics of solvation should not differ for folded vs ID
> peptides.
> > >> You
> > >> > may see behavior with igb=7 that matches your expectations, because
> it
> > >> > tends to give overly solvated, unstructured peptides even when they
> > >> should
> > >> > be folded.
> > >> >
> > >> > You don't mention the protein force field used, which is critically
> > >> > important.
> > >> > On Sep 2, 2013 4:50 PM, "Thomas Evangelidis" <tevang3.gmail.com>
> > wrote:
> > >> >
> > >> > > Dear AMBER community,
> > >> > >
> > >> > > I want to assess qualitatively the interaction potential between
> an
> > ID
> > >> > > protein and ID peptides with implicit solvent (due to the excess
> > speed
> > >> > > gains on GPUs). I am using as a test case a 13mer peptide which
> has
> > >> been
> > >> > > studied with NMR and CD and was found to be unstructured. So far I
> > >> have
> > >> > > tested igb 8 and 7 and I have found 7 to be better. Although 8 is
> > the
> > >> > > latest and is rumoured to be the current standard choice :
> > >> > >
> > >> > > http://archive.ambermd.org/201210/0029.html
> > >> > >
> > >> > > , it folds the peptide to an alpha-helix after ~17 ns of unbiased
> MD
> > >> > using
> > >> > > the parameters quoted at the end of the message. In contrast, when
> > >> using
> > >> > > igb 7 the peptide has some helical propensity but is mostly
> > >> unstructured
> > >> > > (helical and random coil conformations are in equilibrium).
> > >> > >
> > >> > > Does anyone have experience with such kind of systems to suggest a
> > GB
> > >> > > solvation model? Is there any parameter I could tweak to get
> better
> > >> > results
> > >> > > with igb 8 or should I stick to igb 7 ?
> > >> > >
> > >> > > thank you in advance for any suggestion.
> > >> > >
> > >> > > ~Thomas
> > >> > >
> > >> > >
> > >> > > MD Implicit Solvent, infinite cut off
> > >> > >
> > >> > > &cntrl
> > >> > >
> > >> > > ! MOLECULAR DYNAMICS
> > >> > > nstlim=50000000, ! Number of MD-steps to be performed.
> > >> > > dt=0.002,
> > >> > > ntx=1, ! read coordinates and velocities from the restart
> file
> > >> > > irest=0, ! this is not a simulation restart
> > >> > > ntpr=100, ! print energy every 100 steps
> > >> > > nrespa=1, ! evaluate forces every step
> > >> > > ntwr=10000, ! write restart file (.restrt) every 5000 steps
> > >> > > ntwx=1000, ! save coordinates every 5000
> > >> > > ntb=0, ! no PBC with GB solvent
> > >> > > igb=8, ! use the optimized GBn implicit solvent model
> > (ibg=8)
> > >> > > (better than simple GB [igb=1] or OBC[igb=2,5], although less
> > tested)
> > >> > > saltcon=0.15, ! salt concentration
> > >> > > ioutfm=1, ! use binary NetCDF format for the coordinate and
> > >> velocity
> > >> > > trajectory files (mdcrd, mdvel and inptraj).
> > >> > >
> > >> > > ! TEMPERATURE CONTROL
> > >> > > tempi =100.0, ! initial temperature
> > >> > > temp0=310.0, ! reference temperature at which the system is
> to
> > be
> > >> > > kept, if ntt > 0
> > >> > > ntt=3, ! Use Langevin thermostat.
> > >> > > gamma_ln=5, ! Damping coefficient for Langevin dynamics in
> ps -
> > >> 1.
> > >> > > tautp=2.0, ! Time constant, in ps, for heat bath coupling for
> > the
> > >> > > system, if ntt = 1
> > >> > > ig=-1, ! The seed for the pseudo-random number generator
> > >> > >
> > >> > > ! PRESSURE CONTROL
> > >> > > ! ntp=0, ! do not use pressure coupling
> > >> > >
> > >> > > ! BOND CONSTRAINTS
> > >> > > ntc=2, ! bonds involving hydrogen are constrained with SHAKE
> > >> > > tol=1.0e-8, ! Relative geometrical tolerance for coordinate
> > >> > resetting
> > >> > > in shake
> > >> > >
> > >> > >
> > >> > > ! ELECTROSTATICS & VDW
> > >> > > ntf=2, ! ommit force evaluations for bond interactions
> > >> involving
> > >> > > H-atoms
> > >> > > cut=999, ! Cut-off for vdW and electrostatic interactions.
> > >> > >
> > >> > > &end
> > >> > >
> > >> > > &ewald
> > >> > > vdwmeth=1, ! Apply an analytical tail correction to the
> reported
> > >> vdW
> > >> > > energy and virial that is equal to the amount lost due to
> switching
> > >> and
> > >> > > cutoff
> > >> > > ! of the LJ potential.
> > >> > > &end
> > >> > >
> > >> > >
> > >> > >
> > >> > > --
> > >> > >
> > >> > >
> > ======================================================================
> > >> > >
> > >> > > Thomas Evangelidis
> > >> > >
> > >> > > PhD student
> > >> > > University of Athens
> > >> > > Faculty of Pharmacy
> > >> > > Department of Pharmaceutical Chemistry
> > >> > > Panepistimioupoli-Zografou
> > >> > > 157 71 Athens
> > >> > > GREECE
> > >> > >
> > >> > > email: tevang.pharm.uoa.gr
> > >> > >
> > >> > > tevang3.gmail.com
> > >> > >
> > >> > >
> > >> > > website: https://sites.google.com/site/thomasevangelidishomepage/
> > >> > > _______________________________________________
> > >> > > AMBER mailing list
> > >> > > AMBER.ambermd.org
> > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >>
> > >> ======================================================================
> > >>
> > >> Thomas Evangelidis
> > >>
> > >> PhD student
> > >> University of Athens
> > >> Faculty of Pharmacy
> > >> Department of Pharmaceutical Chemistry
> > >> Panepistimioupoli-Zografou
> > >> 157 71 Athens
> > >> GREECE
> > >>
> > >> email: tevang.pharm.uoa.gr
> > >>
> > >> tevang3.gmail.com
> > >>
> > >>
> > >> website: https://sites.google.com/site/thomasevangelidishomepage/
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 03 2013 - 14:00:03 PDT
