Re: SMD constant velocity pulling

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Dec 01 2010 - 10:33:19 CST

Hi Bidisha,

I have being performing SMD with no temperature/pressure control and the
temperature remains constant. You might have to equilibrate the system for
at least a few 100 ps at CPT before you turn it off and then start
pulling. You need to allow for your water box to first relax and adjust
its volume according to the given temperature and volume. Otherwise, if
e.g., the volume is too small, the temperature might increase.

Hope it helps,

             Gianluca

On Wed, 1 Dec 2010, B. Nandy 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 - 05:23:26 CST