Re: SMD constant velocity pulling

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
>>>
>>>
>>> --
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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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