From: Oscar Bastidas (bastidasoh_at_mymail.vcu.edu)
Date: Tue Nov 08 2016 - 15:33:00 CST
Thank you Brian, I'll take a look at these papers.
Oscar Bastidas, Graduate Student
Department of Chemical and Life Science Engineering
Virginia Commonwealth University
On Tue, Nov 8, 2016 at 10:18 AM, Brian Radak <bradak_at_anl.gov> wrote:
> I'm probably fairly off-topic at this point in the thread, but there have
> been quite a few recent papers regarding timesteps and integrators that I
> think might be of interest and also deserve wider attention:
>
> Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
> <http://pubs.acs.org/doi/abs/10.1021/ct5010406>
>
> Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors
> in Equilibrium and Nonequilibrium Simulations of Discrete Langevin Dynamics
> <http://journals.aps.org/prx/abstract/10.1103/PhysRevX.3.011007>
>
> Efficient molecular dynamics using geodesic integration and solvent–solute
> splitting
> <http://rspa.royalsocietypublishing.org/content/472/2189/20160138>
> These are fairly well-defined advancements that would greatly benefit NAMD.
>
> Cheers,
> Brian
>
>
>
> On 11/07/2016 09:21 PM, Peter Freddolino wrote:
>
> Following up on this, I would recommend looking at the standard output and error messages produced by your simulation, which likely include ‘atoms moving too fast errors’ and a crashing simulation due to the timestep being used.
> Best,
> Peter
>
>
> On Nov 7, 2016, at 8:12 PM, Richard Overstreet <roverst_at_g.clemson.edu> <roverst_at_g.clemson.edu> wrote:
>
> Oscar,
>
> You need to do some research on what the parameters you are changing do to the simulation. The integrator time step affects how accurately system trajectories/forces are calculated. I have never seen someone use a 10fs time step before usually this is at most 2fs when the rigidbonds parameter is set to "all". I would recommend reading. "understanding molecular dynamics simulations" by Daan Frenkel before running any more simulations.
>
>
> On 11/07/2016 05:10 PM, Oscar Bastidas wrote:
>
> Hello,
>
> I am trying to run a simulation in NAMD for 100 picoseconds but the output files (*.coor and *.dcd) never show when I execute the simulation for this simulation time. Is there a range of acceptable values for the simulation time parameters (timestep, dcdfreq and total number of runs) that if I go beyond, NAMD will not work? I have successfully run 5 and 10 picosecond simulations by altering those above three parameters in the *.conf file:
>
> for 5 picoseconds:
> Timestep=2 femtosec/step
> dcdfreq=250 steps/trajectory snapshot
> Total run steps=2500 steps
>
> for 10 picoseconds:
> Timestep=2 femtosec/step
> dcdfreq=500 steps/trajectory snapshot
> Total run steps=5000 steps
>
> Both of these scenarios yield results (*.coor and *.dcd files), but when I try to do a 100 picosecond simulation according to the following parameters, I never get my *.coor and *.dcd output files even after waiting for several days:
>
> for 100 picoseconds:
> Timestep=10 femtosec/step
> dcdfreq=1000 steps/trajectory snapshot
> Total run steps=10000 steps
>
> Is there some formula or heuristic to keep in mind when one wishes to alter these variables for longer timescales? Is there another variable that I should alter in the *.conf file in order to run at 100 picoseconds that I may have missed? Thank you.
>
> Oscar Bastidas, Graduate Student
> Department of Chemical and Life Science Engineering
> Virginia Commonwealth University
>
>
> --
> 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
>
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