Hi all. 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 0.00000 0.00000 F CT CT F 3 5.02080 5.02080 0.00000 0.00000 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 0.00000 0.00000 Could anyone give me some help on this issue, please? Thanks a lot to everybody in advance. Sincerally yours, Jones On 7/19/07, George Abadir <[EMAIL PROTECTED]> 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. George 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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