From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Dec 01 2010 - 17:22:40 CST
Thanks Jérôme,
I also prefer Langevin to Berendsen. I might give Lowe-Andersen thermostat
a try in the future. For now, I continue using Langevin thermo+barostat
(except SMD where I use none). Or, do you think I should immediately
switch to Lowe-Andersen since it is the best out there?
Gianluca
On Wed, 1 Dec 2010, Jérôme Hénin wrote:
> Hi Gianluca,
>
> On 1 December 2010 19:49, Gianluca Interlandi <gianluca_at_u.washington.edu> wrote:
>> Hi Jérôme,
>>
>> Sorry, I have another question. What kind of pressure control is recommended
>> to use in conjunction with the Lowe-Andersen thermostat?
>
> In general, I don't know of any requirements. In the particular case
> of NAMD, since there are only two choices of barostat and one of them
> is Berendsen, to me there is really only one choice. I admit that this
> is rooted in heavy personal bias - and an irrational taste for proper
> statistical ensembles. Add to that guilt by association with the
> Berendsen thermostat, and its sinister retinue of flying ice cubes.
>
> Cheers,
> Jerome
>
>> On Wed, 1 Dec 2010, Jérôme Hénin wrote:
>>
>>> Hi Bidisha,
>>>
>>> This sounds like a very good application for the recently implemented
>>> Lowe-Andersen thermostat. It should add virtually no drag.
>>>
>>> Best,
>>> Jerome
>>>
>>> On 1 December 2010 10:51, B. Nandy <nandy_at_physics.iisc.ernet.in> wrote:
>>>>
>>>> Dear NAMD user,
>>>>
>>>> I have question regarding SMD simulation using constant velocity
>>>> pulling.
>>>> I have noticed in different examples that one should switch of the
>>>> constant temperature control during constant velocity SMD pulling. But
>>>> following this method the temperature has increased unreasonably in my
>>>> system. On the other hand using langevin on temperature remains
>>>> constant but I am getting a huge amount of dragging force. So please
>>>> suggest me how to deal with the dragging force when thermostat is on.
>>>>
>>>>
>>>> Thanking you
>>>>
>>>> Bidisha Nandy
>>>> IISc Bangalore
>>>> India
>>>>
>>>>
>>>> --
>>>> This message has been scanned for viruses and
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>>>> believed to be clean.
>>>>
>>>>
>>>
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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