From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jul 03 2018 - 22:37:39 CDT
The short answer is the "seed" parameter in the input file (take a look at the user guide, its in there somewhere). If unspecified, the system clock is used to generate an initial seed for the random number generator. This will take care of initially different velocities. However, NAMD's internal algorithms are not invariant with respect to the order of addition, so in practice if you use more than one core (which you totally should!), very quickly your simulations will diverge even if using the exact same parameters and the same initial velocities. So what you really need to do is collect enough statistics to make a significant inference about if your charges matter. This might mean repeating your simulations multiple times and taking an average.
On 2018-07-03 21:15:00-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
I've been told that NAMD has randomized velocities built in now. If you run a simulation, and then submit that simulation again, the velocities are automatically randomized, is that true? If so, how do I turn that off? I would like to run the same exact simulation again, but only change the partial charges on my ligand. If the velocities are randomized in the same simulation, then I won't know if the partial charges or the new velocities changed my results. I am looking to see how much the different partial charges has an effect on my results. Thanks!
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
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