2016-02-14 4:35 GMT-07:00 Pallavi Banerjee <[email protected]>: > Hello users, > > I am not sure as to how I should interpret the list of exclusions that > csg_dump generates. I have a polymer of 60 beads. I use number of exclusions > as 3 in my topology file. The following is what csg_dump spits out: > > 1 2 3 4 6 > 2 3 4 > 3 4 5 6 8 > 4 5 6 > 5 6 7 8 10 > 6 7 8 > 7 8 9 10 12 > 8 9 10 > 9 10 11 12 14 > 10 11 12 > 11 12 13 14 16 > 12 13 14 > 13 14 15 16 > 18 13 15 16 17 19 20 > 14 15 16 > 15 16 17 20 > 16 17 > 17 19 20 22 > 19 20 21 22 24 > 20 21 22 > 21 22 23 24 26 > 22 23 24 > 23 24 25 26 28 > 24 25 26 > 25 26 27 28 30 > 26 27 28 > 27 28 29 30 32 > 28 29 30 > 29 30 31 32 > 34 29 31 32 33 35 36 > 30 31 32 > 31 32 33 36 > 32 33 > 33 35 36 38 > 35 36 37 38 40 > 36 37 38 > 37 38 39 40 42 > 38 39 40 > 39 40 41 42 44 > 40 41 42 > 41 42 43 44 46 > 42 43 44 > 43 44 45 46 48 > 44 45 46 > 45 46 47 48 50 > 46 47 48 > 47 48 49 50 52 > 48 49 50 > 49 50 51 52 54 > 50 51 52 > 51 52 53 54 56 > 52 53 54 > 53 54 55 56 58 > 54 55 56 > 55 56 57 58 60 > 56 57 58 > 57 58 59 60 > 58 59 60 > 59 60 > > > I don't understand why there are 5/6 beads in one row, when my number of > exclusions is only 3. That is more a question for the gromacs people, but in short "nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away." (from the gromacs manual). So if you have atoms off the side( which are not on the backbone) they will generate more than 3 exclusions.
Christoph > Thanks in advance! > > -Pallavi Banerjee > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
