[gmx-users] problem with thermodynamic integration simulation

Parag Mukhopadhyay tuna_mukho at yahoo.co.in
Thu Jul 21 20:25:34 CEST 2005

I am trying to run thermodynamic integration
simulation to calculate the relative free energy of
slovation between 2-methyl-3-phenylpropylamine( state
A) and 3-phenylpropylamine(state B) by changing carbon
of CH3 (in A) to hydrogen and methyl hydrogen atoms to
dummy atoms (in B)

 For the simulation in water at lamda=1.00 the
molecule if breaking apart. The log file shows
relative constarint deviation after LINCS. However,
the simulation in vacuo (at lamda= 1.00) works fine
and I don't have any problem with any of the
intermediate lamda (and lamda = 0.00) values in either
water or vacuo simulations.

I have tried energy minimizing and then used the
output structure for the md run but it does not help.
I am using OPLS parameters for the molecule (.top file
attached). I have also attached the mdp options I am
using. I will really appreciate any suggestion on how
to fix the problem.

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