From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 12 2018 - 08:38:15 CST
Typically, you only need short time steps for equilibration, when a few of
the forces are still too high. After relaxing the system, you should be
able to bring the time step back up.
On Mon, Feb 12, 2018 at 12:08 AM, Shahee Islam <shaheeislam726_at_gmail.com>
> When i am doing the minimization upto higher steps so that the simulation
> runs at higher time step the water molecule becomes distorted.How i will
> solve the problem.
> On Sat, Feb 10, 2018 at 7:00 PM, Shahee Islam <shaheeislam726_at_gmail.com>
>> I am doing a coarse grained simulation of a protein in NAMD,according to
>> residue base coarse grained tutorial at 340k.I have minimized the system
>> 5000 steps and also i have checked the minimized energy values which
>> converges.But the problem is,when the time step is 10 fs the simulation
>> becomes unstable.
>> ERROR: Atom 456 velocity is 806.693 -1734.92 -2186.46 (limit is 1200,
>> atom 88 of 977 on patch 0 pe 0)
>> ERROR: Atom 457 velocity is -640.392 1941.65 2087.31 (limit is 1200, atom
>> 89 of 977 on patch 0 pe 0)
>> ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
>> patch 0 pe 0).
>> Can anyone please tell me what higher time step value is reasonable for
>> this simulation because when this simulation is done at 3fs the simulation
>> is going smoothly.But the time step 3fs is too low for coarse grained
>> Thanking you
>> Shahee Islam
>> University of calcutta
>> Department of chemistry
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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