SMD and Temperature control

From: snoze pa (
Date: Fri Aug 07 2009 - 15:25:51 CDT

Dear Namd users,

  Thank you very much for your support. I have a question related to
increase of temperature in SMD simulation. I was reading the past
conversation between Sterling, Marcos and Gianluca and observed that
the system temperature actually increases a lot in SMD simulation
compared to what Marcos statement of 20K.

For example, in SMD tutorial provided in the NAMD website(ubiqutin
3-1-pullcv, ubq_ww_pcv.log) , the initial TEMPAVG was 297.5483 which
increases up to TEMPAVG equal to 637.5142 at the end of 20000 step.
This is a huge increase in temperature. Do you think in the example
the system was not properly equilibrated?

Somehow I was luck that my system temperature increases only by 10 and
15 in two SMD simulation.

Thank you


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:08 CST