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

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Tue Feb 13 2018 - 06:56:10 CST

Thank you so much for your suggestions.

On Feb 13, 2018 5:43 PM, "Fotis Baltoumas" <fbaltoumas_at_biol.uoa.gr> wrote:

> Hello,
>
> First of all, check your system's structure, specifically, the particles
> matching the numbers that give the errors. Maybe something there is badly
> modeled and causes the error. Fix it and try again.
>
> Having said that, I would also recommend you consider some of the
> following points:
>
> Try splitting your equilibration phase in different, successive, smaller
> runs with different timestep values, starting at a small value and slowly
> increasing to 10 fs (e.g. 1, 2, 3, 5 and 10 fs for five equilibration
> steps). This is essentially what they do in the CHARMM-GUI martini maker
> for equilibration. If it works and you then manage to start a production
> run with a 10 or 20 fs timestep with no crashes, you're ok.
>
> Have you tried running the equilibration at a lower temperature (300 or
> 310 K) instead of 340 K? I assume that you have reasons for using it, but
> try lowering its value and see what happens. Higher temperature,
> essentially, means extra kinetic energy and that can lead to the "atoms
> moving too fast" crash.
>
> In case your system has proteins in it, are you using any type of
> restraints (e.g. elastic networks, which are often used with Martini)?
> These tend to lead to crashes, especially if they're combined with higher
> temperature values. If so, try simulating your system without the elastic
> network or consider changing its force constant values.
>
> Note that the martini protein force field includes bonds with
> significantly higher constants than the others in some protein side chains
> (these were put there to emulate the constraints of the original Martini,
> which are available in GROMACS but not in NAMD) and, therefore, using an
> elastic network or a high temperature value may be pushing your system to
> its limits.
> Hope I helped,
> Fotis
> On 02/13/2018 01:53 PM, Shahee Islam wrote:
>
> 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
>>>
>>
> --
> *******************************************
> Fotis A. Baltoumas
> Phd Candidate, Bioinformatics Postgraduate Programme
> Department of Cell Biology and Biophysics
> Faculty of Biology, University of Athens
> Panepistimiopolis, Athens 157 01, GREECE
> --------------------------------------
>
> email : fbaltoumas_at_biol.uoa.grhttp://biophysics.biol.uoa.grhttp://bioinformatics.biol.uoa.gr
> *******************************************
>
>

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