Dear Mark, Many many thanks for your kind suggestion. I have also gone through the official Gromacs manual about table potential initially. But I was in a bit confusion.
Thanks again Warm regards Debdas On Tue, Mar 13, 2018 at 1:53 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > I already suggested where to go and find the answer, but you looked > somewhere else... The PDF you linked is kindly contributed by another user, > but not official. Anyway, apparently my memory is wrong and you can't do > what you want. From the reference manual: > > If you want to have different functional forms between different groups of > atoms, this can be set through energy groups. Different tables can be used > for non-bonded interactions between different energy groups pairs through > the .mdp option energygrp-table (see details in the User Guide). Atoms that > should interact with a different potential should be put into different > energy groups. Between group pairs which are not listed in energygrp-table, > the normal user tables will be used. This makes it easy to use a different > functional form between a few types of atoms. > > Maybe you want to check out the whole section there. ;-) > > Mark > > On Tue, Mar 13, 2018 at 5:26 PM Debdas Dhabal <ddha...@seas.upenn.edu> > wrote: > > > Dear Mark, > > > > It would be very grateful if you could please comment on my confusion > > mentioned above. > > > > Thank you very much. > > > > With regards > > Debdas > > > > > > > > On Mon, Mar 12, 2018 at 4:20 PM, Debdas Dhabal <ddha...@seas.upenn.edu> > > wrote: > > > > > Dear Mark, > > > > > > Thanks for your response. Yes, I have gone through that document. > (link: > > > http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf). > > > > > > I have tried using energy-group pairs to take from table file and those > > > are not in the energygrps should take from Gromacs. But the document > says > > > that the remaining interaction should be then calculated from default > > table > > > file named "table.xvg". Hence, in my case, if I only supply pair > > > interaction between *solute-solute* and* solute-solvent* (for which I > > > need to customize interaction) in *"table_solute_solute.xvg"* and > default > > > "*table.xvg"* file respectively. Then Gromacs is taking > *solvent-solvent* > > > interaction (for which I want to use the Gromacs normal thing and I > > haven't > > > given a table file) form that default *"table.xvg"* file. This means > all > > > the remaining interaction (for which I haven't given the table file or > > > didn't mention in the energygrps) is calculated using default > > "table.xvg" > > > file. But this not what I wanted. I want to take solvent-solvent > > > interaction from Gromacs defined LJ potential. > > > > > > At the bottom of the page no 6 of that document also says that > > > "It is important to note however that when a combination of Lennard > Jones > > > and Buckingham terms is required tabulated potentials must be used for > > all > > > the non-bonded interactions even for the Lennard Jones." > > > > > > This means if I use *"vdwtype = User"* then I must have to supply all > the > > > interaction using table file and cannot use both table and Gromacs > > defined > > > potential simultaneously ?. Kindly correct me if I got the meaning of > > that > > > line wrong. > > > > > > I will be waiting for your valuable comments. Thanks so much > > > > > > with regards > > > Debdas > > > > > > On Mon, Mar 12, 2018 at 12:33 PM, Mark Abraham < > mark.j.abra...@gmail.com > > > > > > wrote: > > > > > >> Hi, > > >> > > >> Yes, you can specify which energy-group pairs get which tables, and > > which > > >> do not get any (thus get the normal thing). Did you check out the > > >> documentation yet? > > >> > > >> Mark > > >> > > >> On Mon, Mar 12, 2018 at 5:30 PM Debdas Dhabal <ddha...@seas.upenn.edu > > > > >> wrote: > > >> > > >> > Hello everyone, > > >> > > > >> > Could anyone of you help me regarding the aforementioned problem. It > > >> would > > >> > be very nice of you. > > >> > > > >> > Thanks in advance. > > >> > > > >> > With regards > > >> > Debdas > > >> > > > >> > On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal < > > ddha...@seas.upenn.edu> > > >> > wrote: > > >> > > > >> > > Dear Mark, > > >> > > > > >> > > Thanks so much for your prompt reply. I had gone through that > > manual > > >> and > > >> > > I was able to use two different non-bonded potential for two > > different > > >> > > energy groups using table potential. But my question is a bit > > >> different. > > >> > > May be I was not able to make my question clear. I know the fact > > that > > >> by > > >> > > using table file I can use two different non bonded potential but > > >> what I > > >> > > wanted to ask whether it is possible to use table file only for > user > > >> > > defined potential and not for which Gromacs already have > predefined > > >> > > potential at the same time. > > >> > > > > >> > > Let me make it more clear. I have a system of solute in water. I > > want > > >> to > > >> > > use table file for only solute-water interaction and want to let > the > > >> > > Gromacs take LJ potential for water-water interaction (ie. I don't > > >> want > > >> > to > > >> > > explicitly supply water-water interaction through Table file). In > > >> another > > >> > > way one can ask if I put *"vdwtype=User"* then is it *mandatory* > to > > >> give > > >> > > non-bonded potential for both solute-water as well as water-water > > >> > > interaction through Table file only, or one can only use Table > file > > >> for > > >> > > solute-water and Let the Gromacs take its predefined LJ potential > > form > > >> > for > > >> > > water-water interaction (as in case of vdwtype = Cut-Off case). So > > >> > > basically using Gromacs predefined potential and table potential > at > > >> the > > >> > > same time. > > >> > > > > >> > > I hope I am able to make my question more clearer than before. > > Thanks > > >> > > again for your help. > > >> > > > > >> > > With regards > > >> > > Debdas > > >> > > > > >> > > On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham < > > >> mark.j.abra...@gmail.com> > > >> > > wrote: > > >> > > > > >> > >> Hi, > > >> > >> > > >> > >> Yes, if you check out the documentation of tabulated non-bonded > > >> > >> interactions in the reference manual, you will see that you can > > apply > > >> > >> different tables for particles when drawn from different energy > > >> groups. > > >> > >> > > >> > >> Mark > > >> > >> > > >> > >> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal < > > >> ddha...@seas.upenn.edu> > > >> > >> wrote: > > >> > >> > > >> > >> > Hello everyone, > > >> > >> > > > >> > >> > This question may be very simple to most of the Gromacs user. I > > >> wonder > > >> > >> if > > >> > >> > Gromacs allow us to use both user-defined non-bonded potentials > > >> (Table > > >> > >> > potential) as well as Gromacs predefined potential at the same > > >> time. > > >> > For > > >> > >> > example, if I have a system with a solute in a solvent and for > > >> > >> > solvent-solvent nonbonded interaction, I want to use Gromacs > > >> defined > > >> > LJ > > >> > >> > potential but for solute-solvent nonbonded interaction, I want > to > > >> use > > >> > a > > >> > >> > custom potential using a Table format. I know that > > solvent-solvent > > >> > >> > interaction can also be incorporated in the Table file and we > can > > >> run > > >> > >> > Gromacs successfully, but I want to use Table potential only > for > > >> which > > >> > >> > Gromacs does not have predefined form. Is it possible ?. If > > so, I > > >> > >> would > > >> > >> > be grateful if someone could suggest me to how to do that?. > > >> > >> > > > >> > >> > I will appreciate all your valuable inputs. Thanks so much in > > >> advance. > > >> > >> > > > >> > >> > -- > > >> > >> > Debdas Dhabal > > >> > >> > Postdoctoral Researcher. > > >> > >> > SEAS, Department of Chemical and Biomolecular Engineering, > > >> > >> > The University of Pennsylvania, Philadelphia, PA 19104, USA. > > >> > >> > -- > > >> > >> > Gromacs Users mailing list > > >> > >> > > > >> > >> > * Please search the archive at > > >> > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > before > > >> > >> > posting! > > >> > >> > > > >> > >> > * Can't post? Read http://www.gromacs.org/ > Support/Mailing_Lists > > >> > >> > > > >> > >> > * For (un)subscribe requests visit > > >> > >> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > >> or > > >> > >> > send a mail to gmx-users-requ...@gromacs.org. > > >> > >> > > > >> > >> -- > > >> > >> Gromacs Users mailing list > > >> > >> > > >> > >> * Please search the archive at http://www.gromacs.org/Support > > >> > >> /Mailing_Lists/GMX-Users_List before posting! > > >> > >> > > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > >> > > >> > >> * For (un)subscribe requests visit > > >> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_ > gmx-users > > >> or > > >> > >> send a mail to gmx-users-requ...@gromacs.org. > > >> > >> > > >> > > > > >> > > > > >> > > > > >> > > -- > > >> > > Debdas Dhabal > > >> > > Postdoctoral Researcher. > > >> > > SEAS, Department of Chemical and Biomolecular Engineering, > > >> > > The University of Pennsylvania, Philadelphia, PA 19104, USA. > > >> > > > > >> > > > >> > > > >> > > > >> > -- > > >> > Debdas Dhabal > > >> > Postdoctoral Researcher. > > >> > SEAS, Department of Chemical and Biomolecular Engineering, > > >> > The University of Pennsylvania, Philadelphia, PA 19104, USA. > > >> > -- > > >> > Gromacs Users mailing list > > >> > > > >> > * Please search the archive at > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> > posting! > > >> > > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > >> > * For (un)subscribe requests visit > > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > >> > send a mail to gmx-users-requ...@gromacs.org. > > >> > > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at http://www.gromacs.org/Support > > >> /Mailing_Lists/GMX-Users_List before posting! > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> * For (un)subscribe requests visit > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > >> send a mail to gmx-users-requ...@gromacs.org. > > >> > > > > > > > > > > > > -- > > > Debdas Dhabal > > > Postdoctoral Researcher. > > > SEAS, Department of Chemical and Biomolecular Engineering, > > > The University of Pennsylvania, Philadelphia, PA 19104, USA. > > > > > > > > > > > -- > > Debdas Dhabal > > Postdoctoral Researcher. > > SEAS, Department of Chemical and Biomolecular Engineering, > > The University of Pennsylvania, Philadelphia, PA 19104, USA. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Debdas Dhabal Postdoctoral Researcher. SEAS, Department of Chemical and Biomolecular Engineering, The University of Pennsylvania, Philadelphia, PA 19104, USA. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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