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 - 08:00:07 PST
