[gmx-users] C6 attractive term off OPLSAA
Berk Hess
gmx3 at hotmail.com
Wed Dec 1 17:05:44 CET 2010
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: nishap.patel at utoronto.ca
> To: gmx-users at gromacs.org
> 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" <jalemkul at vt.edu>:
>
> >
> >
> > nishap.patel at utoronto.ca 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 <Mark.Abraham at anu.edu.au>:
> >>
> >>> On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:
> >>>>
> >>>>
> >>>> nishap.patel at utoronto.ca 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 nishap.patel at utoronto.ca:
> >>>>>
> >>>>>> 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" <jalemkul at vt.edu>:
> >>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> nishap.patel at utoronto.ca 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 gmx-users at gromacs.org
> >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>>>>> Please search the archive at
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> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>
> >>> --
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> >>
> >>
> >>
> >
> > --
> > ========================================
> >
> > 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
> >
> > ========================================
> > --
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>
>
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