Thank you, Cristoph. I've added dihedrals to mapping and now it seems to be OK.
Best wishes, Sergey вторник, 17 декабря 2013 г., 20:26:27 UTC+4 пользователь Christoph Junghans написал: > > 2013/12/16 Sergey Larin <[email protected] <javascript:>>: > > > > > > понедельник, 16 декабря 2013 г., 20:04:38 UTC+4 пользователь Christoph > > Junghans написал: > >> > >> 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. > >> > > > > O'K. Thanks. Could you say which atoms are excluded by csg_stat? > Connencted > > by bonds and included in angles and dihedrals? If it so, I'll define > > additional dihedral angles in my simulation and it should solve the > problem. > We follow the Gromacs convention, bonds and angles and dihedrals will > automatically generate exclusion, so adding angles will be fine. > If you use csg_stat without a mapping file the exclusions will be read > from the tpr file, but a mapping reset all exclusions. > > To check your exclusions, you can do something like: > $ csg_dump --top topol.tpr --cg mapping.xml --excl > > Cheers, > > Christoph > > > > Sergey > > > >> 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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. 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