Hi all.<br><br>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:
<br><br>"No default Proper Dih. types, using zeroes"<br><br>Which is quite strange, as the error latelly refers to the following lines:<br><br> CT CT CT F 3 0.65084 1.95253 0.00000 -2.60338
0.00000 0.00000<br> F CT CT F 3 5.02080 5.02080 0.00000 0.00000 0.00000 0.00000<br><br>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 3.3.1 itself:<br><br> CA CT CT NC 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ;<br> CA CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240
0.00000 0.00000<br><br>Could anyone give me some help on this issue, please?<br><br>Thanks a lot to everybody in advance.<br><br>Sincerally yours,<br><br>Jones<br><br><div><span class="gmail_quote">On 7/19/07, <b class="gmail_sendername">
George Abadir</b> <<a href="mailto:georgea@ece.ubc.ca">georgea@ece.ubc.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes of course I looked at the output but I thought is I specify energy<br>groups it will output only those specified and not the whole system.<br>However I tried a short run and it did output both. For the crash it<br>turned out it is because all the nodes try to read the huge trajectory
<br>file at the same time if this may help somebody in the future. We are<br>still trying to figure out how to solve this problem anyway.<br>Thanks for your time.<br>George<br><br>Mark Abraham wrote:<br><br>> George Abadir wrote:
<br>><br>>> Hi all,<br>>> I am running simulations of carbon nanotubes and amino acids<br>>> in water. I need to calculate the potential energies for the whole<br>>> system as well as the interaction energy between the CNT and amino
<br>>> acid. What I am tried to do is to calculate the energy for the whole<br>>> system first (i.e. I did not introduce any energygrps in the run.mdp<br>>> file) and then use the rerun option to calculate the interaction
<br>>> energy after introducing "energygrps= CNT Protein SOL" into the<br>>> run.mdp file. However, each time I try to run this second step the<br>>> cluster on which I run the simulation crashes with a message "Kernel
<br>>> panicked"!<br>>> Does any body know about this problem?<br>><br>><br>> Yeah, something's broken that's probably got nothing to do with<br>> GROMACS, or the fact you're doing a re-run.
<br>><br>>> Is there another way to get both the potential energy of the system<br>>> as well as the interaction potential energy? I understand that if I<br>>> write "energygrps= CNT Protein SOL" from the very beginning the
<br>>> energy of the whole system won't be written, is that right?<br>><br>><br>> mdrun always calculates the total potential and kinetic energy, and<br>> outputs it according to nstxxx flags.<br>> Have you not looked at typical output, or typical .edr file contents?
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