Re: [gmx-users] restart error

y refusing to do appending to the old files. You can make a backup of your files and re-start with mdrun -noappend, but whatever information didn't get written won't be available to you for subsequent analysis. Mark On Thu, Jun 23, 2016 at 2:34 AM ingram <ing...@fhi-berlin.mpg.de>

[gmx-users] restart error

Dear Grommunity, When I try and restart with the command "mpiexec -np 192 mdrun_mpi -v -deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir simann59 simann60 simann61 simann62 simann63 simann64 simann65 simann66 simann67 simann68 simann69 simann70 simann71 simann72 simann73

Re: [gmx-users] Checksum and .log error

are using it is broken. It doesn't look like a gromacs problem... Mark On Thu, 16 Jun 2016 18:54 ingram <ing...@fhi-berlin.mpg.de> wrote: Version 5.1.2 md_golp_vacuo.log is only 207KB md_golp_vacuo.cpt is 97KB md_golp_vacuo.trr is 19MB Im not sure what you mean but the .cpt files were al

Re: [gmx-users] Checksum and .log error

filesystem report for the access times for all the output files? A possible culprit would be a file that is greater than 2GB in size being accessed when that can't work. Mark On Thu, Jun 16, 2016 at 3:03 PM ingram <ing...@fhi-berlin.mpg.de> wrote: Dear Grommunity, I recent

[gmx-users] Checksum and .log error

Dear Grommunity, I recently ran a several simulations that stopped but had not finished. I tried to restart them using mpiexec -np 320 mdrun_mpi -v -deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir simann1 simann2 simann3 simann4 simann5 simann6 simann7 simann8 simann9

Re: [gmx-users] PCA problems

Still no luck When I tried gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -pbc nojump I get a very strange trajectory and covar does not work with this I have also tried gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -fix transxy -pbc mol -s topol.tpr to generate a continuous

[gmx-users] RMSD question

Dear GROMACS community, I am trying to identify the number of unique peptide structures on the surface of a slab. If I simply calculate the RMSD between the protein atoms in each frame of the trajectory this tells me nothing about how these structures compare on the surface as the constraint

Re: [gmx-users] PCA problems

Thanks very much for your help. I have tried with a .tpr file and there is an improvement but still breaks. Similarly when I apply the same protocol as I said previously, but with my peptide unbound I get the same problem however in this case the free peptide has no pbc conditions Best

[gmx-users] PCA problems

Dear GROMACS community I am trying to complete a PCA analysis of my peptide adsorbed to a surface. However when I use : gmx covar -s trajectory.gro -f md_golp_vacuo.xtc and select the protein for both the least squares fit and covariance calculation, followed by gmx anaeig -s

[gmx-users] OpenMP

Dear Grommacs users, I am trying to run some REMD calculations. I did not compile GROMACS with openMP, so when these calculations fail the first error I get is this: Number of logical cores detected (12) does not match the number reported by OpenMP (3). Consider setting the launch

[gmx-users] restarts

Dear GROMITES I have run a simulation that will take longer than a day (longer than my allowed time for one simulaiton on the cluster) I ran the command mdrun -deffnm md_golp Now I'm not sure which .cpt file to use. Two are produced, one called state.cpt and one called md_golp.cpt. They are

[gmx-users] GoIP implementation

Dear GROMACS community, This is not a question directly targeted at the developers but to the wider community. I am trying to implement the GoIP parameters in GROMACS but am struggling to understand which parameters apply to which atoms. If anyone could give me any tips of details of how they

[gmx-users] Fwd: Implementing GoIP parameters in OPLSAA

Dear GROMACS gremlins, I am trying in vain to implement the GoIP parameters for a gold-peptide interface in the OPLSAA ff. I began with just one kind of Au atom and now I want to put in two. When I execute gmx grompp -f em.mdp -c Au111.gro -p topol.top -o em.tpr I get this error Fatal

[gmx-users] Implementing GoIP parameters in OPLSAA

Dear GROMACS gremlins, I am trying in vain to implement the GoIP parameters for a gold-peptide interface in the OPLSAA ff. To begin with I am just trying to get the paramteres working for only a 3x3 Au slab. My .pdb file looks like this: OMPNDNew structure COMPND 1Created by VESTA