Hello I have sent several emails and i am sorry. It is my last attempt to finish this simulation.The molecule i have is C-C-C-C-C-C-O-C-C-O-C-C-O-H or C10H1O3. (ciej molecule) I dont use gromacs librariesthe files i use are attached to the email in which i have descriped step by step the forcefield i use. as you can see in [pairs] i have an extra non Lj 1-4 pair. i did it because the model i use has a potential between atom 10 and 14 ether oxygen and alchohol hydrogen interaction. It is described in the paper as a repulsive energy between these two atoms. and it has a formula: Erepulsive = 3.325789e-7/r^12 the only way to import in gromacs i think is this: [ pairs ]; ai aj funct 10 14 2 0 0 0 0 3.325789e-7 it is an intra-molecular only interaction. so i couldnt think another way to do it except this. as you can see i have several zeros for the charges, C6=o and C12 = 3.325789e-7 fidgeQQ=0 for this case the problem is i get positive total energy. i did this sim for only one molecule just to see what is wrong and i think that coulomb (SR) are wrong for sure. so i want coulomb 1-4 /2 !thats why i put fudgeQQ = 0.5 the values i get at the step 0 are Energies (kJ/mol) Angle Proper Dih. LJ-14 Coulomb-14 LJ (SR) 2.30340e+03 1.08417e+00 3.16570e+00 8.79204e+04 -2.54164e+03 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -2.51250e+00 -4.81042e+04 -2.84931e+04 1.10867e+04 1.84852e+04 Total Energy Temperature Pressure (bar) Cons. rmsd () 2.95719e+04 2.99528e+02 -3.03583e+02 3.13477e-06 tell me please how is this possible thanks in advance and i am sorry once again
ciejbon.itp
Description: Binary data
ciejnb.itp
Description: Binary data
ciej.itp
Description: Binary data
ciej.top
Description: Binary data
-- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
