Re: [gmx-users] convert amber topology and coordinates files into gromacs topology

Tammy, ACPYPE may help you! http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder Best regards 2016-07-03 21:26 GMT-03:00 Ming Tang : > Dear list, > > I am studying glycoprotein. As amber is very slow on CPUs, I really want > to do my simulations in gromacs. I found

[gmx-users] convert amber topology and coordinates files into gromacs topology

Dear list, I am studying glycoprotein. As amber is very slow on CPUs, I really want to do my simulations in gromacs. I found that gromacs has amber99sb.ff. So I want to convert amber topology and coordinates files into gromacs topology using Antechamber. My concerns are: 1) amber16 has

Re: [gmx-users] Fwd: Problem in applying walls in the z direction

I started from the original pdb file without any wrapping. I changed the mdp for the wall settings to: pbc = xy nwall = 2 wall-type = 9-3 wall-density= 5 5 wall-atomtype = OT OT wall-r-linpot = 0.1

Re: [gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

On 7/2/16 8:11 PM, Ming Tang wrote: Thanks Justin, mdrun -rerun works. But I failed to fix it via gmx traj with this command: gmx traj -f traj_comp.xtc -s topol.tpr -ox pullfx.xvg -of pullf.xvg -dt 400 error say .xtc file do not have force information. Is the command I used correct? No,