From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Oct 19 2007 - 00:09:06 CDT
I agree with Jerome. Not that we are lazy and don't want to answer
every single question, but the manual many times is actually very
enlightening -and fascinating, indeed! It is just a matter of patience
and curiosity :).
2007/10/18, Wang, Boyang <bwang9_at_uic.edu>:
> Hi Jerome, thanks a lot for pointing out. I think I have always been
> trying to look for the answer from the "NAMD tutorial", or otherwise
> googling my question, such as "NAMD and damping coefficient" etc. I
> actually didn't pay attention to "NAMD 2.6 user's guide". I will look it
> up next time.Boyang.
>
>
> On Thu, October 18, 2007 10:29 pm, Jerome Henin wrote:
> > Hi Boyang,
> > Sorry for the not-too-nice reply, but I was trying to make a point for
> > the sake of future generations.
> >
> > Maybe you have an oder version of the manual? In the online version,
> > the entry for LangevinDamping says:
> > " If not given, a PDB file is used to obtain coefficients for each
> > atom (see langevinFile and langevinCol below)."
> > http://www.ks.uiuc.edu/Research/namd/2.6/ug/node30.html
> >
> > I don't have previous versions at hand, this might be a recent
> > addition... But as far as I remember the langevinFile option has been
> > there and documented for a long time.
> > Jerome
> >
> >
> > On 10/18/07, Wang, Boyang <bwang9_at_uic.edu> wrote:
> >> Thanks. I have tried. But I did not find a way. Langevindamping is a
> >> system's variable and I can not see how it can have two values in one
> >> run.
> >> Boyang
> >>
> >>
> >> On Thu, October 18, 2007 10:03 pm, Jerome Henin wrote:
> >> > I always ask the same boring question (I must be getting old): have
> >> > you tried the user's guide? Quite a fascinating read, actually.
> >> >
> >> > Jerome
> >> >
> >> >
> >> > On 10/18/07, Wang, Boyang <bwang9_at_uic.edu> wrote:
> >> >> Dear all,
> >> >>
> >> >> I have a quick question about the Langevin damping coefficient.
> >> >>
> >> >> Is there a way to apply 1 ps-1 damping to some atoms and apply 100
> >> ps-1
> >> >> damping to some other atoms in the same system during one run?
> >> >>
> >> >> Thanks a lot!
> >> >>
> >> >> Boyang
> >> >>
> >> >>
> >> >
> >> >
> >>
> >>
> >>
> >
> >
>
>
>
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