Re: [gmx-users] Free energy calculations - desolvation energy of Na+

2010-10-25 Thread Justin A. Lemkul
eva.pluhar...@marge.uochb.cas.cz wrote: Hi Justin, thank you for suggestion about changing the integrator, but I would like to know why it is not possible to sample properly by md under these circumstances. 1. Do you know any papers about sampling efficiency of systems with almost or complete

Re: [gmx-users] Free energy calculations - desolvation energy of Na+

2010-10-25 Thread Justin A. Lemkul
eva.pluhar...@marge.uochb.cas.cz wrote: Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0

[gmx-users] Free energy calculations - desolvation energy of Na+

2010-10-25 Thread eva . pluharova
Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0 = vdw-q couple-lambda1