2013/12/16 Sergey Larin <[email protected]> > > Dear Sikandar, > > Thank you for your help. I've done everything you describe already. I've > prepared mapping and topology files and start test IBI process. I'll try to > describe problem that exists, from my point of view in more details. > Let's use notation proposed by you and see at A-B distribution. Monomer unit > of my polymer consists of 11 beads that have 4 different types: > -C1-D1-A1-D1-C1-B1-A2-B2-B3-A3-B4- > This topology is described in VOTCA mapping file that I use to calculate > distributions with csg_stat. Of course, it excludes interactions for beads > bonded directly. for example, A2-B2 and B3-A3 pairs are not included in > distribution. This is right. But it should also exclude pairs in which beads > are connected by two consecutive bonds, for example, A2-B3 and B2-A3, but > csg_stat does not do this exclusion. That is why I have the peak on the A-B > pair distribution function. And this is a problem. > As far as I know, Gromacs does not calcuate non-bonded interactions for beads > connected by one, two and three consecutive bonds, thus only interactions > between pairs B1-A3 and A2-B4 are calculated during simulation. Thus, only > these two pairs should be taken into account when calculation distribution, > and csg_stat does not do this. > > So, my question is how to exclude 1-3 and 1-4 pairs from distributions > calculated by csg_stat? Is it possible at all? Unfortunately I've not found > any solutions neither in manual, nor in tutorial samples. VOTCA has no way to define the number of consecutive bonds to exclude, but you can create a couple of extra bonds and angles to achieve the same number of exclusions.
Cheers, Christoph > > Sincerely, > Sergey > > > суббота, 14 декабря 2013 г., 0:41:51 UTC+4 пользователь sikandar написал: >> >> Hi Sergey >> >> From your description of the problem, I understand that you want to use >> csg_stat to compute >> only the non-bonded distributions between specified atoms. Right? >> >> If so.. csg_stat can be used to compute both bonded and non-bonded >> distributions separately. >> To achieve that one approach would be to specify your molecule topology that >> each atom has >> unique and different name though there may be multiple atoms of same type. >> In your monomer case, >> there are four different types of atoms A, B, C, D, and each monomer >> consists of 2 As, 3 Bs, 2Cs, and 2 Ds. >> Then, in topology, you can specify atom types as A, B, C, D and atom names >> are A1, A2, B1, B2, B3, C1, C2, >> and D1, and D2. For clarification, you can check out the propane example in >> votca-tutorials. >> >> Now with above mentioned topolopy, you can compute non-bonded distributions >> between A1-A2, C1-C2, and so on. >> >> Next, if you want to perform coarse-graining and need a reference pair >> distributions then first you need to define >> a mapping to specify how to determine CG beads configurations from a given >> reference all-atom configuration. Then >> you can provide this mapping file to csg_stat to determine target >> distributions for coarse-graining. >> Again you can check out propane example and votca manual to get more >> information about how to achieve this. >> >> I hope this helps. >> >> Cheers >> Sikandar >> >> >> On Fri, Dec 13, 2013 at 3:36 AM, Sergey Larin <[email protected]> wrote: >>> >>> Dear votca users, >>> >>> I've faced one more problem (not so big, I suppose) in coarsegrainig using >>> votca. I've found that csg_stat calculate pair distribution functions >>> taking into account atoms that are bonded. As a result the distributions >>> have peaks that correspond to bonded interaction (see the picture, in the >>> molecule I'm coarsegraining the monomer unit is -C-D-A-D-C-A-B-B-A-B-). It >>> is clear for me that it is pretty useless to perform IBI for non-bonded >>> interactions using these distribution as target ones. Thus, my question is >>> how to say csg_stat to exclude bonded atoms from distribution caclulations? >>> Unfortunately, I've found only the way to create exclusion list for >>> non-bonded interactions to perform reference simulations for bonded >>> interactions distributions. >>> >>> Thanks in advance. >>> >>> Sincerely, >>> Sergey >>> >>> >>> -- >>> 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 http://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/groups/opt_out. >> >> > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
