Dear Amber Users,
This is with regard to the usage of the
'iwrap" parameter. I think this is one of the common thread in the
amber mailing list. I checked the list to gather information on it and
it has thrown several views from different users and experts. I
however still have some concern going forward with this parameter and
hence would like to get an opinion from the people in the forum before
I proceed.
I am planning to submit a relatively long simulation of a
protein-peptide system in explicit water. Now I understand that during
the course of the simulation, the complex could diffuse towards the
edge of the primary box and in doing so there might be a situation
where the peptide might protrude out of the primary box. So if I use
"iwrap=1', then the peptide would be wrapped into the primary box from
the other end and hence in visualization of the primary box, i will
see that the protein-peptide molecules are separated. Now I understand
that this is essentially not a problem and can be corrected by
processing the trajectory file using image centering option.
Alternatively I also learn that I can just set "iwrap=0" and in
this case I would not encounter the separation visualization effect of
the protein-peptide system during simulation. However in this case,
the solvent molecules would diffuse which can again be re-centered by
post processing the trajectory.
So my understanding from the mailing list suggest me that
either options should be ok with their respective pros and cons. I am
a bit inclined towards using "iwrap=1" for my simulation. However I am
concerned just in case I encounter some issues later resulting in
loss of resource and time.
So, I will be deeply obliged if the users can kindly throw some
insight in this regard.
Thank you,
Dilraj Lama.
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Received on Wed Feb 15 2012 - 01:30:02 PST
