Re: Re: simulation becomes unstable in residue base coarse grained system

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 12 2018 - 09:20:04 CST

The time needed for equilibration depends on the system, but 200 ns seems a
long time. There is probably something gone wrong in the initial setup of
the system, and you should inspect the frames in VMD, for example looking
at the atoms that give the error (selection by index keyword).

The force field used in the RBCG tutorial is an extremely popular CG force
field, which is easy to use in a variety of other codes besides NAMD. *Hint:
the name of the force field used is in the tutorial title!* Search the
literature for papers that use that model.

Giacomo

On Mon, Feb 12, 2018 at 10:05 AM, SHAHEE ISLAM <islamshahee_at_gmail.com>
wrote:

> 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.
>>
>> Giacomo
>>
>> On Mon, Feb 12, 2018 at 12:08 AM, Shahee Islam <shaheeislam726_at_gmail.com>
>> wrote:
>>
>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> 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
>>
>

-- 
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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