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