Hi David,
Thank for your reply. Some researchers study the viscoelasticity the protein via SMD, and then use Kelvin-Voigt model to fit the strain vs time curve to obtain the Young's modulus and viscosity. Based on the literature, the Lowe-Anderson thermostat is better than the Langevin thermostat in characterizing the viscosity. Lowe-Anderson is perturbs the system dynamics to a far lesser extent than the Andersen method. sadly, it is not available in AMBER.
Thanks.
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, 24 February 2018 12:56:35 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Enquiry on ntt
On Fri, Feb 23, 2018, Ming Tang wrote:
> Thanks for your explanation. I want to study the viscoelasticity of a
> protein in the presence of water in NVT using SMD. Hence, I think I need
> a thermostat in this case. Do you have any suggestion for me?
I'm guessing that most Amber users (i.e. me) typically use diffusion
calculations as a surrogate for viscosity. In addtion, not many Amber users
use SMD (I'm happy to hear that I'm wrong!) So, you'll probably need to look
at the literature, and/or just try some experiments.
....dac
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Received on Fri Feb 23 2018 - 19:30:02 PST
