[gmx-users] C6 attractive term off OPLSAA
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Wed Dec 1 17:13:14 CET 2010
I am going to give that a try. Thanks.
Quoting Berk Hess <gmx3 at hotmail.com>:
>
> 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
>> >>>>>>>
>> >>>>>>> ========================================
>> >>>>>>> --
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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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