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<div>Dear Sabuj,</div>
<div> </div>
<div>It would be difficult to help without more info (size of system, contents of system, .mdp file, etc...). I have not used simulated annealing in years, and when I used the software in the past, it was mostly structure determination from unknown phases (cooling an unknown partial structure from say 450 to 290 and running molreplacement every 10 degrees with several annealed structures, or taking structures from 10 seperate runs for the same thng)...</div>
<div> </div>
<div>If the system (yours) however is 50 degrees over/under or fluctuating this much, it would indicate your equilibrium was not long enough, probably between temperature changes. You could try increasing time segments to 5-20 ns between temperature changes, or run a simple eq, then extended sims for 10-50 ns as seperate runs at a set temperature. As I assume a gaussian distribution, you might have to do multiple runs in either experimental set up, say 3-4 at each temperature, to generate the data with the natural gaussian distribution for kinetics (viscosity, density, etc...).</div>
<div> </div>
<div>Good luck,</div>
<div> </div>
<div>Stephan Watkins, PhD</div>
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Message: 6<br/>
Date: Mon, 25 Jan 2016 18:38:34 +0000<br/>
From: Mark Abraham <mark.j.abraham@gmail.com><br/>
To: gmx-users@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se<br/>
Subject: Re: [gmx-users] Temperature Annealing<br/>
Message-ID:<br/>
<CAMNuMAS=XKGR7DMwW-WGM2-61COw+D8F6CfNjLOfCQKEYhbBew@mail.gmail.com><br/>
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<br/>
Hi,<br/>
<br/>
What fluctuations were you seeing over the time segments?<br/>
<br/>
Mark<br/>
<br/>
On Mon, 25 Jan 2016 19:25 abdus sabuj <sabujbuetche@gmail.com> wrote:<br/>
<br/>
> Dear gmx users,<br/>
><br/>
> I am trying to get viscosity as a function of temperature. So I have put<br/>
> the following annealing inputs to the mdp file.<br/>
><br/>
> ;simulated anneling<br/>
> annealing = single<br/>
> annealing-npoints = 6<br/>
> annealing-time = 0 2000 4000 6000 8000 10000<br/>
> annealing-temp = 300 310 320 330 340 350<br/>
><br/>
> i.e, at 10ns, the temperature should be at 350K, right? But I saw after my<br/>
> npt simulation that, the last temperature reached at 400K. Why that's<br/>
> happening, did I make any mistakes?<br/>
><br/>
> Thanks,<br/>
> Sabuj<br/>
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