From: Brian Radak (bradak_at_anl.gov)
Date: Tue Nov 08 2016 - 09:18:15 CST
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> 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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