[gmx-users] Help with RB dihedrals implementation
Jones de Andrade
johannesrs at gmail.com
Fri Jul 27 04:33:17 CEST 2007
I'm trying to implement a samll RB-potential for some molecules I'm working
with. I choosen to go following the files from opls-aa force field included
with gromacs. Unfortunatelly, I get this error:
"No default Proper Dih. types, using zeroes"
Which is quite strange, as the error latelly refers to the following lines:
CT CT CT F 3 0.65084 1.95253 0.00000 -2.60338
F CT CT F 3 5.02080 5.02080 0.00000 0.00000
And, for a final point that makes my doubt, I don't see any difference
between this lines and this ones from ffoplsaabon.itp from gromacs 3.3.1itself:
CA CT CT NC 3 5.77183 -2.67148 0.95814 -4.05848
0.00000 0.00000 ;
CA CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240
Could anyone give me some help on this issue, please?
Thanks a lot to everybody in advance.
On 7/19/07, George Abadir <georgea at ece.ubc.ca> wrote:
> Yes of course I looked at the output but I thought is I specify energy
> groups it will output only those specified and not the whole system.
> However I tried a short run and it did output both. For the crash it
> turned out it is because all the nodes try to read the huge trajectory
> file at the same time if this may help somebody in the future. We are
> still trying to figure out how to solve this problem anyway.
> Thanks for your time.
> Mark Abraham wrote:
> > George Abadir wrote:
> >> Hi all,
> >> I am running simulations of carbon nanotubes and amino acids
> >> in water. I need to calculate the potential energies for the whole
> >> system as well as the interaction energy between the CNT and amino
> >> acid. What I am tried to do is to calculate the energy for the whole
> >> system first (i.e. I did not introduce any energygrps in the run.mdp
> >> file) and then use the rerun option to calculate the interaction
> >> energy after introducing "energygrps= CNT Protein SOL" into the
> >> run.mdp file. However, each time I try to run this second step the
> >> cluster on which I run the simulation crashes with a message "Kernel
> >> panicked"!
> >> Does any body know about this problem?
> > Yeah, something's broken that's probably got nothing to do with
> > GROMACS, or the fact you're doing a re-run.
> >> Is there another way to get both the potential energy of the system
> >> as well as the interaction potential energy? I understand that if I
> >> write "energygrps= CNT Protein SOL" from the very beginning the
> >> energy of the whole system won't be written, is that right?
> > mdrun always calculates the total potential and kinetic energy, and
> > outputs it according to nstxxx flags.
> > Have you not looked at typical output, or typical .edr file contents?
> > Mark
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