[gmx-users] Temperature for different groups

Hi everybody, I have a small question. I read somewhere that for a better performance on coupling the Temperature of a system is better do it by dividing the system in groups, let say protein and solvent, and coupling them to the same target temperature. Is it remaining true for other integrato

Re: [gmx-users] Free Energy Integrator Selection

Hi there, I am also doing FEP calculations and I am also using sd as integrator. The problem that I am having with this integrator is the temperature coupling (NTP). I am setting the targeted temperature of the system on 300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me 303

[gmx-users] FEP charged molecule cuestion

Hi there, Could someone please share some ideas about the next situation?: I am trying to estimate the relative binding affinity of two small molecules to a protein. In the setup process, ions are added in the solvent to neutralize the system. Then as everybody suggest, the ligand partial charg

[gmx-users] pair types in FEP calculations

Hi there, Could someone please help to understand the use of function types 3 and 2 in the [pairtypes ] directive in the topology file? I am trying to used it in a free energy calculation but the gromacs manual-4.5.4 in the page 112 is kind of confusing. Thanks in advance, Marcelino -- gmx-us