protein-DNA complex

From: Urszula Uciechowska (
Date: Thu Jul 16 2015 - 09:40:25 CDT

Dear Namd users,

I am new to NAMD, I did the minimization for my protein-DNA complex and I
would like to perform the nvt and npt simulation. I followed the tutorial
for 1UBQ and ssb. I performed the minimization step and would like to run
nvt, however I am not sure how to change the file.

For nvt I would like to apply the harmonic restrains to the backbone atoms
(20kcal/molA). I would like to maintain the temperature at 300K by
Langevin dynamics with damping factor equal to 5 (250ps). Could anyone
send me copy of the example of the input file for the nvt and npt

Thank you for any suggestions

best regards

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:58 CST