Re: SMD constant velocity pulling

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Dec 01 2010 - 10:36:07 CST

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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