From: SHAHEE ISLAM (islamshahee_at_gmail.com)
Date: Mon Feb 12 2018 - 09:05:04 CST
Thank you so much for your reply.Can you please tell me after how much time
the simulation will become stable.Because after 200 ns still the atomic
velocity is too fast and system becomes stable, am not getting any
reference from any paper about the equilibration time for residue base
coarse grained simulation in NAMD.
On Feb 12, 2018 8:10 PM, "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com> wrote:
> 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
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