[gmx-users] C6 attractive term off OPLSAA
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Wed Dec 1 16:42:11 CET 2010
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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