[gmx-users] (no subject)

Greetings I have a large protein of 303 residues and one of the lysine is acetylated in the same. The forcefield selection according to the options says as follows: Residue 'ALY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS we

Re: [gmx-users] REMD run on higher nodes.

Mark > > On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal > wrote: > > Greetings > > > > I'm running REMD of 96 replicas where the run.pbs is the following: > > > > #!/bin/tcsh > > #PBS -S /bin/tcsh > > #PBS -l walltime=00:15:00 > > #PBS -q

[gmx-users] REMD run on higher nodes.

Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR se

[gmx-users] REMD run showing temperature range more than the equilibrated.

Hi all ! well, I'm working on REMD with 96 replicas, with temperature range 280K to 425.04K. The NVT equilibration works well and graphs plotted show almost the required temperature after equilibration. Then, after 3 ns of remd run , the edr -> xvg files show initial temperature atleast 40 -50 u

Re: [gmx-users] REMD:subsystems are not compatible.

r set of state_.cpt files is mutually inconsistent after some > crash, because some files were written and some were not. Use gmxcheck to > find out the times. The good news is that the _prev.cpt files will allow > you to construct a self-consistent set. > > Mark > > > On Fri,

[gmx-users] REMD:subsystems are not compatible.

Greetings I'm running REMD with 96 replicas. It has run till 7.3 ns after extending it once using mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend And if i put to restart this again it shows the error: --- Program mdrun_m