Re: simulation becomes unstable in residue base coarse grained system

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Sun Feb 11 2018 - 23:08:42 CST

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>
wrote:

> hello
> 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
> simulation.
> Thanking you
>
> Shahee Islam
> University of calcutta
> Department of chemistry
>

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