2016-02-15 5:12 GMT-07:00 Pallavi Banerjee <[email protected]>: > Thank you, Christoph! > > Also, there seems to be a discrepancy in the calculation of rdfs between > csg_stat and g_rdf. The rdfs obtained from both are different, even on using > the same tpr file as input. > > I am performing iterations over both bonded and non-bonded interactions, > with two types of beads, A and B in my system. Bonded interactions are the > following: bond AB, angle ABA, angle BAB, dihedral BABA. Non-bonded are A-A, > B-B, and A-B. The difference is seen with just the interaction A-B. I am > attaching the rdfs from csg_stat and g_rdf. Could anyone provide the code by > which csg_stat calculates rdf ? What could be going wrong here? I think only attached the xvg file, but not the dist.new files. However, this is hard to debug from the distributions anyhow, so could you send the following files to give us more insight: - settings.xml - conf.gro - topol.top (+ non-standard include files) - grompp.mdp - index.ndx to the mailing list or [email protected] (if you don't like to share them here) or open an issue here <https://github.com/votca/csg/issues>.
Christoph > > Thanks in advance! > > -Pallavi Banerjee > > > On Sunday, February 14, 2016 at 5:05:59 PM UTC+5:30, Pallavi Banerjee wrote: >> >> 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. >> >> 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.
