Re: Difference between REMD replica temperature and actual temperature

From: jozs2019_at_uni.sydney.edu.au
Date: Tue May 29 2018 - 18:19:31 CDT

Hi Norman,

Good catch - no, the thermostat was switched off (but I was minimising for 10ps before beginning REMD). I've just done a short run with the thermostat on and it's looking a lot more like it should now.

Thanks very much!

Jazmin

Jazmin Ozsvar | PhD Candidate
Weiss Laboratory | School of Life and Environmental Sciences | Faculty of Science
THE UNIVERSITY OF SYDNEY
Level 4 East, Charles Perkins Centre | The University of Sydney | NSW | 2006
________________________________
From: Norman Geist <norman.geist_at_uni-greifswald.de>
Sent: Tuesday, 29 May 2018 5:12:11 PM
To: namd-l_at_ks.uiuc.edu; jozs2019_at_uni.sydney.edu.au
Subject: AW: namd-l: Difference between REMD replica temperature and actual temperature

Do you have the langevin thermostat enabled?

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von jozs2019_at_uni.sydney.edu.au
Gesendet: Dienstag, 29. Mai 2018 04:03
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Difference between REMD replica temperature and actual temperature

Hi all,

I've been trying to set up some T-REMD runs and have noticed that the actual temperature reported for replicas appears to be very different to the theoretical replica temperature. For example, I get history files that look like this:

2000 10 356.95 1.571019497206337 -27830.44422562166

4000 11 362.02 1.657781183829707 -27833.337255755807

6000 12 367.17 1.634859540746946 -27831.33867217014

8000 13 372.38 1.605235843972867 -27829.948596293

As far as I know, the third column is the theoretical temperature, whereas the fourth column is the actual temperature - if this is the case, then the difference is huge! I've tried running replicas for a few ns but the results don't really change.

I was wondering whether anyone has seen something similar and could give me some direction for troubleshooting. Or if I'm totally wrong about what the number in the fourth column means, please let me know!

Thanks,

Jazmin

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