Thank you so much for your help. ~M. Chakraborty On Thursday, 25 May 2017 02:49:59 UTC-4, Christoph Junghans wrote: > > 2017-05-24 18:58 GMT-06:00 M. Chakraborty <[email protected] > <javascript:>>: > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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