Re: [gmx-users] Nano-structures equilibration

Thank you very much, Alex. I also performed the process on GPU, and I got the below error: step 1: Water molecule starting at atom 96743 can not be settled.Check for bad contacts and/or reduce the timestep if appropriate.Wrote pdb files with previous and current coordinates WARNING: Listed

[gmx-users] How to convert amber prep and param file to gromac topology file

Hi everyone I have prep and param file for hem.o2 I want to know how I can convert it to itp file thanks -- 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

[gmx-users] can i produce the NO force files for system

hi everyone can i produce the force field for NO nitric oxide that bonded with heme Thanks -- 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/Support/Mailing_Lists

[gmx-users] Regarding grid spacing

Dear All, Which is more appropriate fourier grid spacing for gromos53a6 ff with cutoffs being 0.9 and 1.4nm? 0.16 or 0.12?? I've not seen too many papers with 0.16 being used for this forcefield and that too with cutoffs like 1.0 for rcoulomb and rvdw. Is there any problem if I use fourier

[gmx-users] Checkpoint files error

Dear All, After equilibration, I want to pass on the checkpoint files state.cpt for production run for which I give the command g_mdrun -s md.tpr -c md.gro -o md.trr -cpi state.cpt -cpo state_md.cpt The job terminates with error that output files for checkpoint files are insufficient Just 1 out

Re: [gmx-users] MDrun -maxh option

Hi, Inter-simulation signalling for coordinating stuff like mdrun -maxh for replica exchange has not had a great history. I believe it finally works properly in 2016, but haven't actually tried it. Mark On Sat, Jul 1, 2017 at 3:45 PM Akshay wrote: > Hello All, > >

[gmx-users] MDrun -maxh option

Hello All, The cluster of my University uses a queuing system with a maximum wall-time of 12 hours. So, I run mdrun with the option -maxh 11.9 and subsequently restart the simulation using the output checkpoint files iteratively. However, the -maxh option has not been killing the jobs when I run

Re: [gmx-users] gmx wham problem

Dear Matthew, thanks for your opinion. How can you establish if the histograms are sufficiently overlapped? Is there any thumbs role? For what concern the negative sign of reaction coordinates, I think it could derive from the choice of the order of the pulling groups and the vector along you

[gmx-users] replica exchange

Dear All, I am doing replica exchange for a peptide in water and I used the following command to run my system: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] but I encountered with an error saying: HYDU_create_process (utils/launch/launch.c:75): execvp error on file mdrun_mpi (No such file