[gmx-users] Reg:Equilibration

[Anil Mhashal]

Yeah... A equilibration can be complish within the ps n we have to make
ensure that the there should not be more fluctuation in the potential energy
in other words it should be stabilize.

On 5 October 2010 17:47, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anil Mhashal wrote:
>
>> Just plot a graph of the potential energy with respect to the time and
>> check the energy fluctuation, it should be less than 10% of the average
>> potential energy then u can say that ur protein is equilibrated.
>>
>>
> I would think that, for most systems, a fluctuation of 10% is quite large.
>  I would expect most stable systems to fluctuate less than 1%, if that.
>  Even then, you can judge very little from potential energy alone.  The
> simulation may be stable at that point, but without more analysis, I'd say
> it is hard to judge how equilibrated the system is.  In my experience, the
> potential energy generally converges within a few ps, but other properties
> may take substantially longer to converge.
>
> -Justin
>
>
>> On 5 October 2010 17:16, vinothkumar mohanakrishnan <kmvinoth at gmail.com<mailto:
>> kmvinoth at gmail.com>> wrote:
>>
>>    hi anil
>>
>>    i get the potential energy at the end of the mdrun. if i want to
>>    calulate the deviation with what i should compare and calculate the
>>    deviation.can you be more specific.
>>
>>    Regards
>>    Vinoth
>>
>>
>>    On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal
>>    <anil2000.2008 at gmail.com <mailto:anil2000.2008 at gmail.com>> wrote:
>>
>>         To check ur equilibration, just look at the potential energy
>>        and find out the deviation in the energy if the deviation in the
>>        energy is within 10% then ur equilibration is successful...
>>
>>        On 5 October 2010 14:56, vinothkumar mohanakrishnan
>>        <kmvinoth at gmail.com <mailto:kmvinoth at gmail.com>> wrote:
>>
>>            Hi all
>>
>>            Suppose say i have a box of decane molecules and i want to
>>            equilibrate. say i have all the necessary files to run
>>            mdrun. on what basis i say whether my equilibration is
>>            successful r not after the mdrun. what properties i should
>>            measure to know whether my equilibration was successful.
>>
>>            Regards
>>            Vinoth
>>
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>>        --         Anil R.Mhashal
>>        Research fellow
>>        Physical Chemistry Division
>>        National Chemical Laboratory
>>        Pune
>>
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>> --
>> Anil R.Mhashal
>> Research fellow
>> Physical Chemistry Division
>> National Chemical Laboratory
>> Pune
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Anil R.Mhashal
Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune
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