[gmx-users] angle/distance/position restraints in alchemical free energy calculation

I want to apply distance or angle restraints between any atoms of protein and any atoms of ligand to maintain the initial binding mode of ligand in the protein when non-bonded interactions entirely turned off. As described in figure 1 from the article (http :/

Re: [gmx-users] angle/distance/position restraints in alchemical free energy calculation

On 11/5/17 8:35 PM, minky son wrote: I want to do it using gromacs. Is there any way to control those restraints (except dihedral angle) in gromacs? You can set up any sort of bonded interactions (all of which can be perturbed via the free energy code) using an [intermolecular_interactions

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

I want to do it using gromacs. Is there any way to control those restraints (except dihedral angle) in gromacs? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Sup

Re: [gmx-users] angle/distance/position restraints in alchemical free energy calculation

On 11/3/17 9:36 AM, Wes Barnett wrote: On Fri, Nov 3, 2017 at 2:00 AM, minky son wrote: Dear gmx user, I’m studying about alchemical free energy calculation. I have been read some articles about restraints during free energy calculation, they referred the procedure in the article ( http://pu

Re: [gmx-users] angle/distance/position restraints in alchemical free energy calculation

On Fri, Nov 3, 2017 at 2:00 AM, minky son wrote: > Dear gmx user, > I’m studying about alchemical free energy calculation. > I have been read some articles about restraints during free energy > calculation, they referred the procedure in the article ( > http://pubs.acs.org/doi/pdf/10.1021/jp02178

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

Dear gmx user, I’m studying about alchemical free energy calculation. I have been read some articles about restraints during free energy calculation, they referred the procedure in the article (http://pubs.acs.org/doi/pdf/10.1021/jp0217839). I tried to search mailing list, but still I couldn’t u