From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Nov 07 2016 - 21:21:51 CST
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
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:47 CST