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.
