Re: [AMBER] Langevin thermostat different gamma_ln giving systematically different energies?

From: Thomas Cheatham <tec3.utah.edu>
Date: Sun, 17 Jan 2021 02:23:48 +0000

>From your e-mail it is difficult to interpret - your average energies seem to be the same (-75,000) but the standard deviations are different (which is not unexpected - if you add randomized changes more frequently, more likely more deviation) but perhaps I am misunderstanding.

--tec3

________________________________________
From: Liao <liaojunzhuo.aliyun.com>
Sent: Saturday, January 16, 2021 6:44:16 PM
To: AMBER Mailing List
Subject: [AMBER] Langevin thermostat different gamma_ln giving systematically different energies?

Dear Amber community,

Iíve been testing out the effect with different gamma_ln values (0.1, 2, 5, 10) using a Langevin thermostat, and what I found with my system (NPT, using ntf=7 only evaluating non-bonded forces, giving my protein a weight restraint of 100 so that itís as fixed as possible) was that different random seeds with the same gamma_ln give very close average energies from the MD output (-75000+-5), while different gamma_ln values give different average energies(-75000+-500). The runs are over 100 ns and the averages seemed to be converged pretty well within each gamma_ln value, while they are systematically different between different gamma_ln.

Is this difference in energy expected? Because itís undesired for my tests here. Could it be something specific with my system thatís causing this?

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Received on Sat Jan 16 2021 - 18:30:02 PST
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