From: Radak, Brian K (bradak_at_anl.gov)
Date: Mon May 09 2016 - 10:12:01 CDT
What was your initial command sequence? Something like:
should have done what you wanted.
Personally, I don't think heating is particularly necessary for many biological systems unless you have a clearly low temperature crystal structure. Even then, relaxing the system with RMSD restraints would seem to obviate the need for gradual heating (and also make possible solvent annealing at relatively high temperatures).
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From: dhirajks_at_gmail.com [dhirajks_at_gmail.com]
Sent: Sunday, May 08, 2016 11:21 AM
Subject: Re: namd-l: gradual heating problem
I solved the problem, i was initializing velocity by temperature using reinitvels command but i was using first time step as last time step of minimization. Setting first time step as 0 solved the problem.
However as you said you dont heat below 250 k, so do you heat your system before equilibration and after minimization. 250 and 310 k are not that different. If i am not heating below 250, do i have to heat my system at all if i want to do my simulation at 310K.
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On May 8, 2016, at 11:04 AM, Brian Radak <bradak_at_anl.gov<mailto:bradak_at_anl.gov>> wrote:
How did you initialize velocities? The thermostat does not control initial conditions.
Also, it's very hard to hold most systems at such low temperature - normal dynamics should repartition potential energy into kinetic energy very quickly.
I stopped heating from temperatures below 250 K or so a long time ago because the system would often naturally heat up faster than my increment (it's hard to say if your choice of 100 steps will overcome this). I generally only use these kinds of protocols for annealing up to 600 K or so and then ramping down the temperature afterward.
On 05/08/2016 10:27 AM, Dhiraj Srivastava wrote:
I am trying to gradually heat my system after minimization and using the following set of commands.
no where else in the entire configuration file i can see number 310. however after starting the calculation, system is going right away to 310 kelvin. I looked at previous post but could not find satisfactory answer. How can I resolved this issue?
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov<mailto:brian.radak_at_anl.gov>
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