[gmx-users] RE:C6 attractive term off OPLSAA
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Dec 2 01:57:56 CET 2010
On 2/12/2010 7:40 AM, nishap.patel at utoronto.ca wrote:
> Would I change the sigma to negative in my nb.itp file the way it is
> set or do I need to include a [nonbond_params] section and make sigma
> negative in that specific section? because I realize from the manual
> OPLS-AA uses combination rule 3 but in the manual it shows to combine
> sigma for i and j using rule 2 and rule 1 and 3 correspond to C6 and
> C12 for i and j. Is that correct?
This is too convoluted for me to understand :-)
Mark
>
> Quoting nishap.patel at utoronto.ca:
>
>> 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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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>
>>>>
>>>>
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>
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