Re: namd simulation

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Thu Mar 05 2015 - 04:46:29 CST

Dear Urszula,

For the protein-dna MD i suggest for equilibrium run NPT and for production run NVT will be ok, however, it depends on you what you want to do, you should read some papers about what you want to achieve, then try MD, meanwhile you may try tutorials, the tutorials provide enough information to start and learn. And for restating your MD you will also understand it after doing tutorials, it is suggested that dont jump direct to any MD rather practice some tutorials provided. I had also started in this way.

regards

Abhi

________________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Urszula Uciechowska <urszula.uciechowska_at_biotech.ug.edu.pl>
Sent: Tuesday, March 3, 2015 10:20 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: namd simulation

Hi,

I am new to namd. I run minimisation for a protein-DNA system and would
like to carry on with the NPT or NVT, which simulation should I select?
How to use the coordinates form the previous step?

best regadrs
Urszula

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