After trying all suggestions ( :D ), you (Abhishek) can try to validate
your protocol by running dt=0.001 and dt=0.004 (with hmass repartitioning)
for tiny system (e.g Ala3) to get converge data (about few hundreds ns),
then histogram CA distance between residue 1 and 3.
If two runs (dt=0.001, dt=0.004) produce similar distribution, your
protocol is fine.
Hai
On Wed, Nov 16, 2016 at 11:04 AM, David Cerutti <dscerutti.gmail.com> wrote:
> If your nstlim is that high then you are not in serious danger from random
> seed bugs. The problem is that the NET force imparted to each particle by
> Langevin thermostating tends towards zero as 1/sqrt(nstlim). If nstlim is
> 10000 you'll see a big problem, 100000 you'll see a problem but may not
> notice it, and 1000000+ the effect is negligible. Still, ig = -1 is
> usually a good policy unless you are intent on exactly reproducing a
> trajectory, it which case you should set ig to a specific sequence of
> numbers (i.e. 8572, 8573, 8574, ...) for each segment.
>
> Dave
>
>
> On Wed, Nov 16, 2016 at 10:58 AM, Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Hi,
> > I guess you must first try what Daniel and Dave have suggested, maybe
> you
> > can play around with the gamma_ln values later when you rule out
> everything
> > else.
> > all the best.
> >
> > Regards
> >
> > *Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
> > [image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in
> >
> > Website: http://www.elvismartis.in <http://www.elvismartis.in/>
> > group website: http://www.profeccoutinho.net.in/
> > Address:
> >
> > Kalina, Santa Cruz [E]
> > , Mumbai, 400 098, INDIA
> >
> > Alt. e-mail: emartis12.live.com
> > <https://in.linkedin.com/in/elvisadrianmartis>
> >
> >
> > On 16 November 2016 at 21:25, Thakur, Abhishek <axt651.miami.edu> wrote:
> >
> > >
> > > Elvis thank you for such a quick response I am using default value for
> > > gama_ln. so I guess it must be 0. Do you suggest someother value that I
> > > should define>
> > >
> > >
> > > David I don't think that I am using ig=-1, do you recommend me to try
> > with
> > > that?
> > >
> > >
> > >
> > > This is the script I am using in both case,
> > >
> > > Just with the difference of time step
> > >
> > >
> > > imin=0,irest=1,ntx=5,
> > > nstlim=2500000,dt=0.004,
> > > ntf=2,ntc=2,ntb=0,
> > > igb=8,cut=9999.0,rgbmax=25.0,
> > > ntpr=500, ntwx=500, ntwr=10000,
> > > saltcon=0.2,
> > > temp0=300.0,
> > > ntt=1,tautp=1.0,
> > > nscm=0,ntxo=2,
> > >
> > >
> > >
> > > ________________________________
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Sent: Wednesday, November 16, 2016 4:46:06 AM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] HMassRepartition
> > >
> > > These are both very short runs, and without knowing any other details
> > > (assuming you have done everything correctly) I would expect the dimer
> to
> > > open with 1fs time steps soon enough. Just to make sure, are you
> running
> > > with a clock-based or otherwise varying random seed? I don't know what
> > the
> > > status of all our bulletproofing is, but if you're running with ascii
> > > restarts then there could still be a way to get repeating pseudo-random
> > > sequences into your system which would tend to unfold proteins if the
> > > restarts occur frequently enough (or cause milder "opening" effects if
> > the
> > > restarts happen less frequently).
> > >
> > > Dave
> > >
> > >
> > > On Wed, Nov 16, 2016 at 10:38 AM, Thakur, Abhishek <axt651.miami.edu>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I have carried out two different GB/SA simulation, igb=5 and all the
> > > > parameters same
> > > >
> > > > 1. With HMassRepartition with dt=0.004 and in 20ns I found that my
> > dimer
> > > > opened.
> > > >
> > > > 2.Simple Gb/SA with dt=0.001 and in 20ns I have found my dimer has
> not
> > > > moved at all.
> > > >
> > > >
> > > > I cannot get the reason behind this, as both have same duration of
> > > > simulation. Can this be possible or I have done some mistake>
> > > >
> > > >
> > > >
> > > > Thanking you,
> > > >
> > > > Abhishek
> > > > _______________________________________________
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Received on Wed Nov 16 2016 - 08:30:03 PST
