[gmx-users] Reg:Equilibration

[Anil Mhashal]

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.



On 5 October 2010 17:16, vinothkumar mohanakrishnan <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>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>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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>
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-- 
Anil R.Mhashal
Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune
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