[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
>>>>>>>>>>
>>>>>>>>>> ========================================
>>>>>>>>>> --
>>>>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>>> Please search the archive at
>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at    
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>





More information about the gromacs.org_gmx-users mailing list