Hi, Maybe it is not so clear from the topology table in the manual, but when you supply sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params section also expects sigma and epsilon. So it seems you could not set only C6 to zero. However there is an, undocumented, trick: if you use a negative sigma, C6 is set to zero.
Berk > Date: Wed, 1 Dec 2010 10:42:11 -0500 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] C6 attractive term off OPLSAA > > I see. I actually want to compare my RDFs with C6 term off. Earlier I > tried using force.c code file and turned C6 = 0, but when i compared > my RDFs, it didn't look any different so I am not sure if it even > worked at all or made any difference to the simulation, but again I > was using OPLS-AA and the nb.itp file itself does not indicate value > for C6 or C12. > > If there any other way I could achieve this? > > > > Quoting "Justin A. Lemkul" <[email protected]>: > > > > > > > [email protected] wrote: > >> I ran the simulation using a different force field ffG53a6. I > >> modified the ffG53a6nb.itp file by changing the term C6 to zero for > >> nonbonded parameters, but this time for urea in water. The > >> simulation ran fine without any warning or exploding. I don't > >> understand why it would work with one force-field and not with > >> OPLS-AA. > >> > > > > I don't understand why it worked at all, frankly, but more than likely > > you've been lucky enough to make 53a6 work, but OPLS-AA failed. You're > > making significant alterations to the nonbonded interactions of the > > system. > > > >> Also using mdrun -rerun, I would basically use the nb.itp file with > >> nonbonded parameters as mentioned earlier and everything else is > >> the same i.e. my .mdp parameters and do another run using my > >> previous trajectory file? I tried to look through some of the posts > >> for using -rerun but I don't understand how that would not still > >> blow up the system. I would like to give it a try for sure but I am > >> not quite sure how I would use the command as such. > >> > > > > Using mdrun -rerun recalculates energies from an existing trajectory. > > You would generate a trajectory with a normal force field model, then > > create a new .tpr file that has your modified potential, such that you > > can decompose the energy terms cleverly. If your goal is to generate > > trajectories to study the effects of using a modified potential (i.e., > > C6 = 0), then you can't use -rerun. > > > > -Justin > > > >> I really appreciate the help. > >> > >> Thanks. > >> > >> > >> Quoting Mark Abraham <[email protected]>: > >> > >>> On 1/12/2010 5:06 AM, Justin A. Lemkul wrote: > >>>> > >>>> > >>>> [email protected] wrote: > >>>>> I tried using the nonbonded parameters as defined below in my > >>>>> ffoplsaanb.itp file for methanol in water and this is the syntax > >>>>> I used: > >>>>> > >>>>> [nonbond_params ] > >>>>> ;i j func c6 c12 > >>>>> opls_154 opls_111 1 0.00E+000 2.43E-006 > >>>>> opls_154 opls_112 1 0.00E+000 0.00E+000 > >>>>> opls_154 opls_112 1 0.00E+000 0.00E+000 > >>>>> opls_155 opls_111 1 0.00E+000 0.00E+000 > >>>>> opls_155 opls_112 1 0.00E+000 0.00E+000 > >>>>> opls_155 opls_112 1 0.00E+000 0.00E+000 > >>>>> opls_156 opls_111 1 0.00E+000 2.70E-007 > >>>>> opls_156 opls_112 1 0.00E+000 0.00E+000 > >>>>> opls_156 opls_112 1 0.00E+000 0.00E+000 > >>>>> opls_157 opls_111 1 0.00E+000 3.01E-006 > >>>>> opls_157 opls_112 1 0.00E+000 0.00E+000 > >>>>> > >>>>> When I tried to do mdrun, I got an error saying my system is > >>>>> exploding. I tried doing the mdrun without nonbonded parameters > >>>>> and it runs fine. So I am not sure if I am using the > >>>>> nonbond_params concept correctly. i.e. I want C6 to be zero > >>>>> between my solute (methanol) and solvent (water). This is the > >>>>> error: > >>>>> > >>>>> Warning: 1-4 interaction between 2 and 6 at distance 3.786 which > >>>>> is larger than the 1-4 table size 2.500 nm > >>>>> These are ignored for the rest of the simulation > >>>>> This usually means your system is exploding, > >>>>> if not, you should increase table-extension in your mdp file > >>>>> or with user tables increase the table size > >>>>> > >>>>> Suggestions? > >>>>> > >>>> > >>>> Your implementation of your concept is technically correct, but > >>>> perhaps physically unreasonable. You're turning off the > >>>> attractive LJ component and leaving only a repulsive component. > >>>> It sounds about right that everything is flying apart. > >>> > >>> Indeed. The way to do this is with mdrun -rerun on a trajectory > >>> generated with the normal version of the forcefield, as I think I said > >>> in another thread yesterday. > >>> > >>> Mark > >>> > >>>> > >>>> -Justin > >>>> > >>>>> Thanks. > >>>>> > >>>>> -Nisha P > >>>>> > >>>>> Quoting [email protected]: > >>>>> > >>>>>> Okay I am going to give it a try. I just wanted to make sure I was > >>>>>> calculating C6 and C12 correctly as well using sigma and epsilon > >>>>>> according to rule 3 > >>>>>> > >>>>>> C12 = Sigma^(6)*C6 > >>>>>> C6 = 4*sigma^(6)*epsilon > >>>>>> > >>>>>> Thanks > >>>>>> > >>>>>> > >>>>>> Quoting "Justin A. Lemkul" <[email protected]>: > >>>>>> > >>>>>>> > >>>>>>> > >>>>>>> [email protected] wrote: > >>>>>>>> Hello, > >>>>>>>> > >>>>>>>> I have a concern regarding C6 attractive term in LJ > >>>>>>>> potential. I am using OPLS-AA force field, and I wish to > >>>>>>>> turn off attractive term C6 by setting the parameters to > >>>>>>>> zero. One of the suggestion was to add a [nonbond_params] > >>>>>>>> in my ffoplsaanb.itp file and set the C6 to zero between > >>>>>>>> the non-bonded pair. In my system for example, which > >>>>>>>> consists of one methanol in water, I wish to set C6 term to > >>>>>>>> zero between my solute and solvent. Since OPLSAA is all > >>>>>>>> atom force field it treats each atom individually and has > >>>>>>>> sigma and epsilon for each atom, so I am not sure how I > >>>>>>>> would actually set my nonbond_params in my nb.itp file. I > >>>>>>>> realize I need to convert each sigma and epsilon to C6 and > >>>>>>>> C12, so say for example for methanol in water my > >>>>>>>> [nonbond_params] would look something like this? > >>>>>>>> > >>>>>>>> [ nonbond_params ] > >>>>>>>> ; i j func c6 c12 > >>>>>>>> CT OW 1 0.00 calculated value for C12 here? > >>>>>>>> CT HW1 1 0.00 > >>>>>>>> CT HW2 1 0.00 > >>>>>>>> > >>>>>>>> CT is the carbon in Methanol. OW, HW1 an HW2 correspond to > >>>>>>>> atoms in TIP3P water model > >>>>>>>> > >>>>>>>> Is that correct? Would I have to do that for each atom in methanol? > >>>>>>>> > >>>>>>> > >>>>>>> Sounds about right to me. > >>>>>>> > >>>>>>> -Justin > >>>>>>> > >>>>>>>> Any suggestions would be appreciated. > >>>>>>>> > >>>>>>>> Thanks. > >>>>>>>> > >>>>>>>> Nisha P > >>>>>>>> > >>>>>>> > >>>>>>> -- > >>>>>>> ======================================== > >>>>>>> > >>>>>>> Justin A. Lemkul > >>>>>>> Ph.D. Candidate > >>>>>>> ICTAS Doctoral Scholar > >>>>>>> MILES-IGERT Trainee > >>>>>>> Department of Biochemistry > >>>>>>> Virginia Tech > >>>>>>> Blacksburg, VA > >>>>>>> jalemkul[at]vt.edu | (540) 231-9080 > >>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >>>>>>> > >>>>>>> ======================================== > >>>>>>> -- > >>>>>>> gmx-users mailing list [email protected] > >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>>>>> Please search the archive at > >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>>>>>> Please don't post (un)subscribe requests to the list. Use the www > >>>>>>> interface or send it to [email protected]. > >>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>> > >>>>> > >>>>> > >>>> > >>> > >>> -- > >>> gmx-users mailing list [email protected] > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> Please don't post (un)subscribe requests to the list. Use the www > >>> interface or send it to [email protected]. > >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > >> > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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