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

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

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] correlation function

Jamie Seyed wrote: Dear all, Is there any tool in gromacs that can calculate time correlation function ??? R(x,y,z). Many Thanks in Advance/Jamie Yes, various tools can calculate (auto)correlation functions. See manual section 7.4 and appendix D. Mark ___

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

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 ; Maximum number

[gmx-users] correlation function

Dear all, Is there any tool in gromacs that can calculate time correlation function ??? R(x,y,z). Many Thanks in Advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

Re: [gmx-users] pbc = xyz with mdrun -pd ?

Chih-Ying Lin wrote: Hi I am setting pbc = xyz ; and type the commands grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated => the simulation failed and .out file suggested me to use the flag -pd. grompp_mpi -

[gmx-users] pbc = xyz with mdrun -pd ?

Hi I am setting pbc = xyz ; and type the commands grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated => the simulation failed and .out file suggested me to use the flag -pd. grompp_mpi -v -f minim.mdp -c 6LYZ-

Re: [gmx-users] Problem with running MD

Lili Peng wrote: Hi Justin, I do not think that the storage space is an issue because I had submitted another job to the queue (system of one molecule) yesterday, and it's almost near completion. My xtc file is ~4700 kB, trr file is ~22MB, and tpr file ~130MB. I've also checked my *.log f

Re: [gmx-users] Problem with running MD

Hi Justin, I do not think that the storage space is an issue because I had submitted another job to the queue (system of one molecule) yesterday, and it's almost near completion. My xtc file is ~4700 kB, trr file is ~22MB, and tpr file ~130MB. I've also checked my *.log files and nothing seems a

Re: [gmx-users] error no default LJ-14 type

Without seeing the .top and getting a little background on what you've done to prepare said topology, it's hard to say. Generically, you haven't properly accounted for the atom types in the 1-4 interactions, hence grompp can't assign these LJ-14 types. Are you by any chance following my tut

[gmx-users] error no default LJ-14 type

hello gromac m trying to simulate KALP-15 in DPPC. when m running grompp command it shows the following error. Generated 837 of the 2346 non-bonded parameter combinations ERROR 0 [file "dppc.itp", line 112]: No default LJ-14 types ERROR 0 [file "dppc.itp", line 113]: No default LJ-14 types E

Re: [gmx-users] Problem with running MD

Lili Peng wrote: Hi all, I am having a problem while running an MD simulation on a system of 11 identical molecules solvated in a 50nm X 50 nm X 50nm box with Na+ ions. I submit my job, and it starts to run successfully. However, after 2500ps, the xtc and trr files do not increase in siz

[gmx-users] Problem with running MD

Hi all, I am having a problem while running an MD simulation on a system of 11 identical molecules solvated in a 50nm X 50 nm X 50nm box with Na+ ions. I submit my job, and it starts to run successfully. However, after 2500ps, the xtc and trr files do not increase in size anymore, which I presu

[gmx-users] gmx-list digest

Hi all, In what way is gromacs list digest actually formed? How the system decides that the time to form and send the list digest comes? During the last days I got many digests (more than 5 ones a day) many of which contained only 1 or 2 messages, that seems quite inconvenient. Maybe it's reasona