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

2014-03-17 Thread Valentina
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 charges: couple

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

2014-03-14 Thread Dr. Vitaly Chaban
Hi Valentina - Honestly, I did not get the considerations with charges. TI probably scales interaction energies between selected groups, not charges. Science-wise, I would first decouple organic particle, then decouple chloride anions, and place a right sign between these two free energies. If y

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

2014-03-14 Thread Valentina
Hello, I need an advise on how it is better to approach the ThermoD integration of such system: +vely charged inorganic layer, filled with water and counterbalanced by -ve organics Do I integrate out organics both VdW and Coulomb, making the system have total +ve charge at lambda = 1 OR: Do I i