Re: [gmx-users] domain decomposition errors

id van der Spoel wrote: > pedro alberto valiente flores wrote: > > Hi gromacs users: > > I' am trying to run a MD simulation of PlmII+Inhibitor system in cubic > > box (59002 atoms) with gromacs 4.0.5 on 8 processors, but my simulation > > crashes. In attach are fi

[gmx-users] domain decomposition errors

n the simulation without problems in 2 processors (PlmII +PepstatinA_equilibration.log). Can I fix this error setting domain decomposition parameters of mdrun. I going to appreciate any suggestions, -- MC Pedro Alberto Valiente Flores Centro de Estudios de Proteínas Facultad de Biología Universid

[gmx-users] problems compiling gromacs 4.0.5 in Ubuntu 9.0.4

mpi the program works fine In addition if I execute the commands as root they work fine too. How can I fix this problems? sincerely best regards, -- MC Pedro Alberto Valiente Flores Centro de Estudios de Proteínas Facultad de Biología Universidad de La Haba

Re: [gmx-users] C-terminal amide capping

Hi Anita: you can create the topology of your last residue with CONH2 an example is a LYS-CONH2 I name this residue as LYN, you must include this residue in aminoacids.dat, ff.rtp [LYN] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB

Re: [gmx-users] Difference between command pdb2gmx and pdb2gmx_d

Hi Peggy: the difference between comand an comand_d is that comand is with gromacs compile in single precision and comand_d the program is compile in double precision. cheers, pedro On Tue, 2009-02-17 at 14:56 -0800, Peggy Yao wrote: > Dear all, > > In the manual, almost all commands have 2 versi

[gmx-users] compiling gromacs

/openmpi/lib -L$HOME/software/fftw/lib/" --program-suffix=_403_mpi --enable-shared but i have this error in the config.log file conftest.c:19:2: error: #error not catamount -- MSc. Pedro Alberto Valiente Flores. Centre for Protein Studies. Biology School. Havana University. Calle 25 # 45