2017-05-24 18:58 GMT-06:00 M. Chakraborty <[email protected]>: > Thank you for your prompt response. I have attached the cgtop.top file. I > was trying to figure out what to add to the . top file and added the > [defaults] segment. The initial output from csg_gmxtopol started from > [moleculetype]. Thanks again. I think, there is an "[ atomtypes ]" block missing before "[ moleculetype ]", just have a look at any coarse-grained topol.top in the tutorials, e.g. <https://github.com/votca/csg-tutorials/blob/master/propane/ibi/topol.top#L16>.
Christoph > > On Wednesday, 24 May 2017 17:08:13 UTC-4, Christoph Junghans wrote: >> >> 2017-05-24 14:11 GMT-06:00 M. Chakraborty <[email protected]>: >> > I am trying to use the tabulated potential (for non-bonded interactions) >> > obtained from force-matching to run coarse-grained simulation in >> > gromacs. To >> > obtain the topology file I have used csg_gmxtopol. conf_cg.gro file was >> > obtained by running csg_map. In order to use the tabulated potential for >> > simulation, I have made the following changes to the mdp file: >> > vdwtype = User >> > coulombtype = User >> > energygrps = A B >> > energygrp_table = A A B B >> > >> > >> > I must mention here that I have mapped methanol molecules into >> > coarse-grained particles having two beads representation (A for CH3 and >> > B >> > for OH). When I run the command, gmx grompp -v -f cg_grompp.mdp -p >> > cgtop.top >> > -c conf_cg.gro, I get the following error: >> > Fatal error: >> > Syntax error - File cgtop.top, line 4 >> > Last line read: >> > '[ moleculetype ]' >> > Invalid order for directive moleculetype >> > >> > I am not sure what is going on here. I am attempting to run a >> > coarse-grained >> > simulation for the first time. It would be really helpful if someone can >> > guide me to identify what is wrong with my approach. >> The output of csg_gmxtopol is only meant as a template and "File still >> needs to be modified by the user" (from --help output). >> >> Can you post your cgtop.top and we might be able to help? >> >> Christoph >> >> > >> > Thank You. >> > >> > M. Chakraborty >> > >> > -- >> > 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. -- 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.
