[gmx-users] Free energy perturbation of Cu(I) binding

Hi all, Thank you for the help till now and I successfully generated the forcefield Cu(I) binding protein. Now I wanted get the structure of non-copper bound form which I think I can do by perturbing the charge on Cu(I) and even perturbing the bonded and nonbonded parameters. Is there a

[gmx-users] RE: Normal mode analysis

Hi All, I am doing normal mode analysis. After getting the eigen frequencies, is there a way we can visualize the vibrational modes in gromacs. And even how to know which frequency corresponds to which mode of vibration. I saw that IED is used

[gmx-users] Normal mode analysis

Hi All, I am doing normal mode analysis. After getting the eigen frequencies, is there a way we can visualize the vibrational modes in gromacs. And even how to know which frequency corresponds to which mode of vibration. I saw that IED is used to visualize normal modes by integrating it

[gmx-users] Simulation of difloromethane

Hi all, I am just running a test simulation for normal modes. I am unable to create a topology file for diflormethane as gromacs say "unrecognized MOL residue type". I created it manually but now it says " Invalid order for directive moleculetype, file ""topol.top"", line 17". Please t

[gmx-users] Interactions between tow chains of a protein

Hi All, I am abhigna. I wanted to simulate a protein which binds to Copper. Copper interacts with amino acids of Chain A and B of the Dimeric protein. When I convert the pdb file to topology file this is how it defines with A and B with protein and C and D with Copper. So I need to define