Hi Jemerie,
SGLDg (isgld=3) needs sgft and/or sgff, but not tempsg. Sgft is the lambda in the SGLD-GLE paper. (lambda is not the tempsg/temp0 ratio)
In addition to the momentum guiding factor sgft or lambda, SGLDg can use the force guiding factor, sgff, to reduce the energy barrier. When sgff=0, SGLDg is the same as SGLD-GLE.
Sorry for the confusion in document. I will fix it before next release.
Regards,
Xiongwu Wu
> -----Original Message-----
> From: Jérémie Knoops [mailto:jeremie.knoops.gmail.com]
> Sent: Wednesday, October 21, 2015 1:45 AM
> To: AMBER Mailing List
> Subject: [AMBER] SGLDg
>
> Dear Amber users,
>
>
> In a generalized self-guided langevin dynamics (ntt=3, gamma_ln>0 and
> isgld=3), which of the following parameters is required: sgft,sgff, tempsg?
> If I understand it well the guiding factor lambda in the "Self-Guided
> Langevin Dynamics via Generalized Langevin Equation" paper (DOI:
> 10.1002/jcc.24015) is defined in amber by the tempsg/temp0 ratio. sgft and
> sgff do not seem to be used for SGLDg. But it's not clear in the manual for
> me, 2 sentences look contradictory: "sgff Force guiding factor for SGLDg or
> SGMDg" and "sgff is effective for SGMDg".
> Is it right?
>
> Does the TIP3P solvent have to be included in the SGLD region or excluded
> from it?
>
> Thank you,
>
> Jérémie Knoops
>
>
> *PhD Student*
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Received on Wed Oct 21 2015 - 09:00:04 PDT
