[gmx-users] C6 attractive term off OPLSAA
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Wed Dec 1 16:19:27 CET 2010
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.
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.
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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