You can build a system that contains the same number of waters (and
ions) as your protein simulation, compute its average volume and
subtract it from the protein simulation average volume.
g.
>> Dear all,
>>
>> I'm wondering if there is a command in AMBER to calculate the volume of a
>> protein from the trajectory. Specifically, I want to calculate the average
>> volume of the protein from the last 10 ns trajectory. Any suggestions on
>> this issue would be greatly appreciated.
>>
>> Thank you very much for your help,
>> Surasak
>>
>>
>>
>>
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Feb 28 2012 - 07:00:02 PST
