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

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Mon Feb 12 2018 - 09:27:03 CST

Ok.I will try.
Thanking you

On Feb 12, 2018 8:51 PM, "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com> wrote:

> 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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