[gmx-users] RE:C6 attractive term off OPLSAA
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Wed Dec 1 21:40:26 CET 2010
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?
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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>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
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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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