From: Sonu Kumar (sonu2kd_at_gmail.com)
Date: Mon Aug 22 2016 - 15:21:48 CDT
I have a simple polymer molecule of 3 polyethylene chain(200 carbons atoms
each) which are in a box of about 36 Angstroms. However, as per the density
calculations it must be in a box of 25 Anstroms if Periodic Boundary
Conditions are applied.
To shrink it, I followed two approaches :
1. Constant Pressure - Reducing Pressure till the box becomes small. Didn't
help because the polymer will come out (even though WrapAll is on). Hence,
it went out of the box at a certain 30 Anstroms roughly. I had created a
check point around 30 Angstroms and decreased the size of periodic box.
Moreover, two errors were very frequent namely, periodic cell has become
too small for the periodic box conditions and error in rattle algorithm.
2. Colvars - Shrinked the molecule to about 32 Angstroms and then it was
the same story.
Can anyone tell me how to put the molecule in the box such that I don't
encounter rattle algorithm error which is because of the strain in the
input file. Moreover, if I am wrong in my approach, can you please point it
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