Re: [gmx-users] GPU metadynamics

Dear Albert to run parallel jobs on multiple GPUs you should use something like this: mpirun -np (number of parallel sessions on CPU) mdrun_mpi .. -gpu_id so you will have 4 calculations for GPU. Jacopo Inviato da iPad Il giorno 15/ago/2013, alle ore 10:56, Albert ha sc

[gmx-users] replica exchange and gpu

or do I need 8 GPUs. Thanks Jacopo Jacopo Sgrignani PhD Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131 Milano (Italy) email: sgrigna (at) gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] decomposition

Dear all i'm trying to run a MD simulation using domain decomposition but after two days i'm only able to get this error: There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 2.37175 nm Change the number of nodes or mdrun option -rcon or -d

[gmx-users] print force

Dear all could you suggest me a procedure to print the force acting on a atom from a trr file in a human readable format. Thanks a lot Jacopo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] add zinc in gromacs/cpmd

In the list i found infos about an error i can find working with gromacs/cpmd, the Zinc atom is not in the source code. Can anybody help me to what number i have to put in the codo to correctly add this atom. Thanks Jacopo ___ gmx-users mailing list

[gmx-users] gromacs QM/MM

Hi I would like to use the gromacs/Gaussian03 interface and i would like to know if there are any papers with data obtained using this interface. Thanks a lot Jacopo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

[gmx-users] gromacs trajctory mmpbsa

Dear gromacs user, I would like to perform an MMPBSA calculation of a proetin ligand complex using a gromacs trajectory, but this is the first time I try to do it so I have some questions. Did anybody use the Amber-MM-PBSA script with gromacs trajectory? I tried to transform the gromacs traj usi

[gmx-users] Double or single precision

Hi, can anybody explain me the different uses for the single and the double precison packages. Are there situations that explicitly require a double precision package, and situations when i can use a single precision? Thanks a lot Jacopo ___ gmx-users ma

[gmx-users] gmx-cpmd

Hi I tried to use the cpmd-gmx interface with the files in the qmmm-examples folder. I'm able to run grompp but when i Try to run mdrun i can get this message: CPMD calcualtion only supported with CPMD. I tested the two programs indipendently and they seem to work fine. I put all the requested f

[gmx-users] QM/MM cpmd

Hi, I'm trying to use the CPMD/GROMACS qm-mm interface but when i try to run one of the example h20 dimer i can get this error: Fatal error: CPMD calculation only supported with CPMD. Does anybody help me? thanks Jacopo ___ gmx-users mailing listg

[gmx-users] Gromacs-MPI cygwin

Hi, I would like to compile gromacs using cygwin and mpi on a machine running win2003 server, with two quad-core processor. Does anybody experince in this type of situation. I have some problem compiling mpi, becouse I'm able to run the configure script with "without-romio" option, but the process

[gmx-users] Distance restraint

Hi, I have a system with a protein and two different ligands. I'm trying to use distance restrain to hold the ligands inside the protein during a free energy calculation. If I use the distance restrains only between the protein and the first ligand I don't get any error, but if I introduce restrai

[gmx-users] FEP

Hi, I would like to perform free energy perturbation using gromacs. I found some tutorial about this type of calculation, but a question is not clear. My calculation is very similar to the calculation described in the tutorial, because I want to change only the non bonded terms. I didn't understan