Hi,
Did you use appropriate collision frequency (gamma_ln=???) to mimic the
damping effect of solvent?
This could be important since you are using implicit solvation, without
accounting for the damping effect of the solvent such artifacts may result.
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]
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Alt. e-mail: emartis12.live.com
<
https://in.linkedin.com/in/elvisadrianmartis>
On 16 November 2016 at 21:08, 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 - 08:00:04 PST
