[gmx-users] How to examine our created topology

Faezeh Pousaneh fpoosaneh at gmail.com
Sat Feb 14 11:22:29 CET 2015

Dear expert,

I have created topology for an unstudied (simulation) molecule, and I can
run it successfully.

1- How many or which quantities at least must be checked with experiment to
become sure of the created topology? and if we find some difference with
experiment, to what percent this differences can be acceptable? (for
instance, if the experimental value of the density is 920 kg/m^3, is 1000
kg/m^3 OK?).

2- If we intend to improve the differences with the experimental values,
what are the best ways? is changing slightly the charges on the atoms can
be a good way (let us say we correctly have defined bonds, angels, ect
according to the force filed)?

Thank you in advance,
Best regards

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