From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Dec 01 2010 - 11:40:25 CST
Hi Gianluca,
If the temperature does not change, then obviously the thermostat is
not needed. But SMD is all about performing nonequilibrium work, so
you expect some amount of dissipation. I suppose it depends on pulling
speed, how long the SMD is run, and the size of the water bath.
Cheers,
Jerome
On 1 December 2010 17:36, Gianluca Interlandi <gianluca_at_u.washington.edu> wrote:
> Hi Jerome,
>
> I have a question here, since I have been thinking about whether I should
> run SMD with or without CPT in the future. Is a thermostat necessary during
> SMD? In my pull runs with no temp/pressure control, both remain pretty much
> constant.
>
> Thanks,
>
> Gianluca
>
> 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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>>>
>>>
>>
>>
>
> -----------------------------------------------------
> 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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