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.
