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

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Tue Feb 13 2018 - 05:53:23 CST

Comparing the namd parameters value with the published paper's value ,I did
not get any solution. Changing the langeving damping value 5(according to
other paper),still I am getting the same error:atomic velocity is too
fast.Can anyone please help me how I can solve this problem.
Thanking you

On Feb 12, 2018 8:57 PM, "Shahee Islam" <shaheeislam726_at_gmail.com> wrote:

> 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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