From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Dec 01 2010 - 16:55:20 CST
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
>>> dangerous content by MailScanner, and is
>>> 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.
> -----------------------------------------------------
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:49 CST