I'm just loading the trajectory in ptraj and using "image center" on the
whole thing.
My guess is that there's a better way.. Any suggestions would be very
much appreciated.
Thanks in advance
Sasha
Carlos Simmerling wrote:
> if you do the imaging properly (centering the protein first!) then you
> should not see this. tell us what you're doing in detail.
>
> On Thu, May 5, 2011 at 12:03 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>
>
>> Hi all,
>> I'm running simulations of small proteins in mixed solvent. The very
>> common problem I'm seeing is the protein being out of the solvent box
>> after the post-simulation image operation. Since I'm looking for protein
>> surface solvation patterns, this makes life somewhat difficult.
>> Is there a way to stack several of these unit cells to get a complete
>> solvation picture for the protein? Alternatively, is there a way to keep
>> the protein within the bounds of the box.
>>
>> Thanks for any advice
>>
>> Sasha
>>
>>
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Received on Thu May 05 2011 - 14:30:03 PDT
