Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2013-09-17 Thread Justin Lemkul
On 9/17/13 7:26 AM, mabbasi wrote: Dear All users used OPLS ff for my system After md production i get this error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated How to solve the problem ?? St

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2013-06-11 Thread Justin Lemkul
On 6/11/13 10:55 AM, Dr. Vitaly Chaban wrote: On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote: This problem indeed happens from time to time. With versions 4.5+ it is more frequent than with ve

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2013-06-11 Thread Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul wrote: > > > On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote: > >> This problem indeed happens from time to time. With versions 4.5+ it is >> more frequent than with versions up to 4.0.7. It is not always connected >> to >> blowing up in the sense of bad

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2013-06-11 Thread Justin Lemkul
On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote: This problem indeed happens from time to time. With versions 4.5+ it is more frequent than with versions up to 4.0.7. It is not always connected to blowing up in the sense of bad contacts, positive potential energy, etc. The more cores you use per jo

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2013-06-11 Thread Dr. Vitaly Chaban
This problem indeed happens from time to time. With versions 4.5+ it is more frequent than with versions up to 4.0.7. It is not always connected to blowing up in the sense of bad contacts, positive potential energy, etc. The more cores you use per job, the more likely this error to appear. The larg

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2013-06-11 Thread Justin Lemkul
On 6/11/13 1:30 AM, Souilem Safa wrote: Dear Gromacs users, I tried to do the simulation of a single molecule in cyclohexane, I'm using gromos 53a6 force field for both molecules. i did all the minimization steps. After npt, I runned for 25 000 000 steps. just after around 100 000 steps, the

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2012-11-06 Thread Justin Lemkul
On 11/6/12 10:42 PM, Ali Alizadeh wrote: Dear All users I used OPLS ff for my system and I did not break my bonds, When i use gromos96 45a3 after minimizing my bonds break(i can see em.gro) but i do not get any errors in this step Bonds do not break during MD. Probably what you're seeing

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2009-08-20 Thread Mark Abraham
Chih-Ying Lin wrote: Hi In the system, one lysozyme + TIP3P water. After the two commands, grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR pr.mdp, minim.mdp and the error information is as follows. nsteps = 5000

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

2009-08-20 Thread Justin A. Lemkul
Chih-Ying Lin wrote: Hi In the system, one lysozyme + TIP3P water. After the two commands, grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR pr.mdp, minim.mdp and the error information is as follows. nsteps = 5000