[gmx-users] Pull error message

Hi, I am running MD simulation in approximately 1.25x1.25x1.25 nm box containing 64 waters and one LiF ion pair in NpT ensemble using gromacs 4.5.5 version. I am constraining the distance between ions using pull code and printing out force: ; COM PULLING pull = constraint pull

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

Hi Justin, thanks for this link: http://lists.gromacs.org/pipermail/gmx-users/2003-June/006054.html It clearly says, why sampling by MD is not proper. Best, Eva >> Hello all, >> >> I am trying calculate desolvation free energy of Na+ in water using >> option >> couple-moltype, not by creatin

[gmx-users] Re: gmx-users Digest, Vol 78, Issue 186

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 completely switched off particles? How does it depen

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

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