[gmx-users] freezegrps changing coordinates in NPT simulations

Hello again, I'm running a simulation with graphene as a periodic molecule. I've frozen the carbons in place in the mdp file using: freezegrps = CG_CE freezedim= Y Y Y but when I run an NPT simulation, the entire system shrinks (including moving the carbons

[gmx-users] question about REMD

Hello I am running REMD of 53 replica. First I want to equilibrate them. mpirun -np 106 mdrun_mpi -s topol.tpr -v -multidir REMD[012345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152] I always received the error message:

Re: [gmx-users] energy minimization problem

Dear Justin, could you please tell me how to get the maximum force of an exact atom? I tried g_traj -of, but did not get any force data. Thanks a lot. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se]

Re: [gmx-users] energy minimization problem

On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full

[gmx-users] Carbon Nanotube `Y-Junctions'

Dear Gromacs users , Greetings .I am looking for XYZ or PDB file of Carbon nanotube ' Y-junction' . I will be grateful if you can let me know how i can find or make it . Thanks in advance .Best ,Saeed.  -- Gromacs Users mailing list * Please search the archive at