[gmx-users] protein-ligand interaction energy for oligomers

Dear gmx-users, I am working on a hexameric protein. I have done simulation of protein-ligand complex (hexameric i.e. 6 protein monomers and 6 ligands). I want to compare the interaction energy of protein-ligand (energygroups= protein ligand sol) with the biochemical data (delta H). The protein-lig

Re: [gmx-users] time of simulation

On Sat, 2009-07-25 at 15:16 -0700, mahmoud wrote: > Hello Dear GMX Users, > > > I have installed Gromacs 4 on a QUAD computer by Fedora 11. > > When I do not use the "mpirun -np 4 g_mdrun ... " command, just one > CPU is used. > When I use the "mpirun -np 4 g_mdrun ... " command, all of the 4

[gmx-users] time of simulation

Hello Dear GMX Users,     I have installed Gromacs 4 on a QUAD computer by Fedora 11.   When I do not use the "mpirun -np 4 g_mdrun ... " command, just one CPU is used. When I use the "mpirun -np 4 g_mdrun ... " command, all of the 4 CPUs are used.   But the problem is that the time of simulation,

[gmx-users] How to know the electrostatic potential at a given coordinate?

Hi everyone   I wish to know the electrostatic potential for any given position in my system (3-D). g_potential seems only calculate the sum potential in a slice of a simulation box. So is there any way to obtain the entire potential map for a system by existing gromacs tools?   Thanks in advan

Re: [gmx-users] pull.ppa doesn't work

Problem solved, thanks a lot! accomp lin wrote: > > hi everyone, > > I;m using umbrella sampling to calculate PMF > > My system is DPPC + water + protein > In pull.ppa, I set runtype = umbrella ，reftype = com_t0， > K1   = 5000  ，Pos1  = 0.0 0.0 6.0 >