Re: how to apply different damping coefficients simultaneously to different atoms in the same system.

From: Wang, Boyang (bwang9_at_uic.edu)
Date: Thu Oct 18 2007 - 22:44:09 CDT

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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