OK, the problem is likely to arise from constant volume conditions which
I had in my MD simulation. Now that I processed constant pressure
trajectory, the box looks as it should.
Thanks again to Tom
Grzegorz
>> You likely need to image not only the waters, but everything else.
>> Additionally, if you have multiple solute molecules, these can become
>> separated as has been discussed extensively in the archives and
>> tutorials and/or the solute may diffuse out of the primary unit
>> cell. If you image only the waters, the solute may still be outside
>> the primary unit cell.
>>
>> Basically, to get back to the system you expect (i.e. solute
>> surrounded by solvent) you want to center your region of interest
>> (solute) and then image everything not just the waters (as in the
>> commands above).
>>
>> center .P mass origin
>> image origin center
>>
>> --tom
>>
>>
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Received on Wed Jul 27 2005 - 12:53:01 PDT
