[gmx-users] Free energy calculation of a charged system

Valentina valentina.erastova at durham.ac.uk
Mon Mar 17 14:18:05 CET 2014

Hi! Thank you for reply.

You have lost me there, tbh.

I think I didn't make it clear, I have either organic -vely changed molecule
or Cl-. Those counterbalance the +vely charged material. Therefore, I either
have organics or clorine. So, if I do TI and completely decouple vow and

couple-intramol          = yes   
couple-lambda0           = none
couple-lambda1           = vdwq

but then, obviously, I run into problems when simulating charged system (i.e
it crashes)

so, I am thinking of running:

couple-intramol          = yes   
couple-lambda0           = none
couple-lambda1           = vdw

i.e. keeping the charge to balance and having total charge 0 of the
simulation box.

Then the plan would be:

Org -ve                TI          -ve charge remains              TI               
Cl -ve
Material +ve       ---->             Material +ve                 ----->      
Material +ve

Does this make sense? Or it is possible to go from Organics to Cl- directly
in one integration sequence?

Thank you for your advises,

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