Re: protein-DNA complex

From: Vlad Cojocaru (
Date: Thu Jul 16 2015 - 10:59:19 CDT

Hi Urszula,

Well, I believe you should fist come up yourself with draft input files
for NPT and NVT based on reading the NAMD manual very carefully (all
sections regarding standard simulations) and based on the tutorials
which provide you with very useful information. Normally, upon reading
all info available and doing (some of) the tutorials, everything should
be clear and you should be able to easily generate the files you want.
Should you have more specific questions after generating your inputs,
I'd be happy to help ...

Best wishes

On 07/16/2015 04:40 PM, Urszula Uciechowska wrote:
> 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
> simulations?
> Thank you for any suggestions
> best regards
> Urszula
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]

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