From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed May 20 2015 - 11:07:42 CDT
Ok, I dug around in the code a bit. The relevant parts look to be in
ParallelIOMgr.C, and indeed it looks like it will always remove COM
motion upon restart. Look for simParameters->comMove. By default, that
variable is false, which means we will be adjusting it so the restart
will have 0 com motion, and there should be a string "REMOVING COM
VELOCITY" in the namd logfile on restart. You'd turn this behavior off
by setting *COMmotion yes*in the restart configuration file.
On 05/20/2015 10:59 AM, Michael Feig wrote:
> Hence my statement about running on a single core ... and the Berendsen thermostat does not use random seeds.
> Otherwise there are possibly two related options in NAMD:
> Only the latter should be relevant but it is turned off in our simulations.
> If NAMD does remove drift upon restart (which it seems it does) and there is a way to turn it off, we would be happy to learn how to accomplish that.
> The question of why there is drift (or not) is a good one and exactly the reason why this issue is coming up. If we need to run long simulations to see a drift but cannot do so without NAMD removing the drift at every restart it is difficult to diagnose ... we do understand the issues otherwise.
> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: Wednesday, May 20, 2015 11:49 AM
> To: NAMD list; Michael Feig
> Subject: Re: namd-l: Restarting trajectories
> On Wed, May 20, 2015 at 9:47 AM, Michael Feig <feig_at_msu.edu> wrote:
>> To come back to the different trajectory topic raised by Grzegorz and
>> maybe clarify things:
>> We do understand issues about the chaotic nature of MD simulations but
>> it seems that a ‘short’ simulation, let’s say for 10 ps running on a
>> single core should be identical
> please note that the parallelization and load balancing methodology used in NAMD will likely change the order in which forces are summed even when running on a single processor. like it stated before, unless you use fixed point math and no thermostat, you cannot expect trajectories to be perfectly reproducible and reversible.
>> whether it is run as a single run or restarted in between. If that is
>> not the case with NAMD, it means that the frequency of restarts
>> affects the trajectory one obtains.
>> Moreover, we seem to see that every restart leads to some kind of
>> reset in system drift which means that the results are actually
>> different depending on how often
>> simulations are restarted. We seem to see this with the Berendsen
>> thermostat where (Langevin) random seeds should not play a role.
>> The next step for us would be to dig into the NAMD code to see what is
>> going on, but I think there may be a problem here.
> have you checked the NAMD documentation whether there is an option to remove the COM motion upon (re)start?
> i wouldn't be surprised if this may be active by default and would need to be disabled if you want to preserve the center of mass motion.
> but in any case, i don't think removing the COM drift on restart should be a big issue, but rather what part of your simulation setup is *causing* it, since that should not happen under normal circumstances.
> please also note that unlike langevin, a berendsen thermostat will not dissipate a drift but is more likely to enhance it (since *all* velocities are scaled by the same factor thus having the largest error on the fastest atoms).
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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