From: snoze pa (snoze.pa_at_gmail.com)
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.
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