Re: [gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

2013-11-12 Thread Justin Lemkul
On 11/12/13 12:14 PM, cjalmeciga wrote: The output of energy minimization was Potential Energy = -1.42173622068236e+06 Maximum force = 9.00312066109319e+02 on atom 148 Norm of force = 2.06087515037187e+01 OK, reasonable enough. How about a description of what the system is, whi

[gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

2013-11-12 Thread cjalmeciga
The output of energy minimization was Potential Energy = -1.42173622068236e+06 Maximum force = 9.00312066109319e+02 on atom 148 Norm of force = 2.06087515037187e+01 Thanks Javier Justin Lemkul wrote > On 11/12/13 10:58 AM, cjalmeciga wrote: >> I run >> >> grompp -f nvt.mdp -c em.gr

Re: [gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

2013-11-12 Thread Justin Lemkul
On 11/12/13 10:58 AM, cjalmeciga wrote: I run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and everything looks fine. I check the nvt.tpr, and temperature is ok. The fact that grompp completes indicates there is nothing syntactically wrong with the input files. Whethe

[gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

2013-11-12 Thread cjalmeciga
I run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and everything looks fine. I check the nvt.tpr, and temperature is ok. the real problem is with the mdrun function. could be a problem of the software? Thanks Javier Justin Lemkul wrote > On 11/11/13 11:24 AM, Carlos