[gmx-users] number of water molecules affects the PMF

Ozge Engin ozge.engin at gmail.com
Wed Jun 2 09:49:04 CEST 2010

Hi Chris,

The two setups were different from each other in terms of only the number of
water molecules. Even the starting
conformations for the two peptides were the same. I especially took care
about that to leave only the number of molecules as a variable.

I calculated the error by dividing the whole data to 4, and calculated the
standard deviation between the 4 sets, and divided the result by sqrt (3).

For the Xavier's suggestion: I think I should wait a little, at least until
having the same length of trajectory for the two sets.


Ozge Engin
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