[gmx-users] 'fudgeQQ' parameter in the topology file

Dear Gromacs user, I read from the Gromacs Manual (version 5.1.2) that, while fudgeLJ is used only when generate pairs is set to ‘yes’, fudgeQQ is always used. 1. If I set fudgeQQ = 0.0, will gromacs annulate the 1-4 interactions ? 2. If I explicitly insert a (Coulomb 1-4) scaling factor in my

[gmx-users] 'fudgeQQ' parameter in the topology file

Dear Gromacs user, I read from the Gromacs Manual (version 5.1.2) that, while fudgeLJ is used only when generate pairs is set to ‘yes’, fudgeQQ is always used. 1. If I set fudgeQQ = 0.0, will gromacs annulate the 1-4 interactions ? 2. If I explicitly insert a (Coulomb 1-4) scaling factor in my

[gmx-users] gmx sasa versus g_sas

Hi Gromacs users, I am using gromacs tool g_sas to calculate protein excluded volumes and I noticed that it provides significant different excluded volume values when compared to the new version gmx sasa tool. Does anyone know the reason of this and which of the two tool is more reliable? Thanks i