[gmx-users] Questions about free energy calculation tutorial
gozde ergin
gozdeeergin at gmail.com
Fri Nov 4 13:35:01 CET 2016
> If you want the hydration free energy of SDS, you should not include Na+ because the simultaneous decoupling will include the hydration free energy of Na+. You can subtract that out, but there is error associated with that calculation and accounting for that is not necessarily easy. It is straightforward to just deal with SDS alone.
Yes this is exactly what I want but I did not get how the Na+ would be included simultaneously?
My SDS.itp file contains C12H25SO4- molecules, Na+ is not inside this file. There is another SOD.itp file that contains Na+.
So if I only write SDS to couple-moltype in .mdp file, it will decouple C12H25SO4- but not Na+.
Should I put Na+ atom inside the SDS.itp?
> On 04 Nov 2016, at 12:51, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 11/3/16 10:56 AM, gozde ergin wrote:
>>> You can decouple atomic and molecular ions, there are just additional considerations like an interface potential to calculate. See, e.g. work by Benoit Roux.
>>
>> Yes I can but do I need to? I just want to know the free energy of solvation of SDS. If I do not include the Na ion decoupling, is it wrong?
>>
>
> I
>
> -Justin
>
>>> On 02 Nov 2016, at 12:42, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 11/1/16 9:02 AM, gozde ergin wrote:
>>>>>> This is a generic simulation failure message, indicating that your system is blowing up. This could be due to any number of reasons, but without more details it's pointless to guess.
>>>>
>>>> If I do not include the Na ion in decoupling I do not have this warning.
>>>> If I do not decouple Na ion still I need to make the charge of this molecule zero otherwise system charge becomes +1.
>>>>
>>>>>> Decoupling the Na+ ion will mean your resulting dG value includes the hydration free energy of Na+, which it doesn't sound like you're interested in.
>>>>
>>>> My purpose is doing the same thing with SDS that you did with Methane. And as SDS has Na ion I thought I need also to decouple it.
>>>> Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
>>>> Last question even if I do not decouple the Na ion I need to make it charge zero, right?
>>>>
>>>
>>> You can decouple atomic and molecular ions, there are just additional considerations like an interface potential to calculate. See, e.g. work by Benoit Roux.
>>>
>>> -Justin
>>>
>>>> Thanks in advance.
>>>>> On 01 Nov 2016, at 13:21, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On 11/1/16 7:31 AM, gozde ergin wrote:
>>>>>> Hi Justin,
>>>>>>
>>>>>> I would like to ask one question related to this tutorial. I do the same thing with using SDS (Sodium dodecyl sulfate) molecule.
>>>>>> As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate part. However in order to estimate the free energy of SDS salvation in water I need to decouple the all SDS molecule. Since couple-moltype accept only one types of molecule, I hacked the topology and put all atoms I want to decouple in the same [moleculetype] :
>>>>>>
>>>>>> [ moleculetype ]
>>>>>> ; name nrexcl
>>>>>> SDS 3
>>>>>>
>>>>>> [ atoms ]
>>>>>> ; nr type resnr residu atom cgnr charge mass
>>>>>> 1 SL 1 SDS S 1 0.000 32.0600 ; qtot 1.330
>>>>>> 2 OSL 1 SDS OS1 2 0.000 15.9994 ; qtot 1.050
>>>>>> 3 O2L 1 SDS OS2 3 0.000 15.9994 ; qtot 0.400
>>>>>> 4 O2L 1 SDS OS3 4 0.000 15.9994 ; qtot -0.250
>>>>>> 5 O2L 1 SDS OS4 5 0.000 15.9994 ; qtot -0.900
>>>>>> .
>>>>>> .
>>>>>> 25 HAL2 1 SDS H71 25 0.000 1.0080 ; qtot -1.090
>>>>>> 26 HAL2 1 SDS H72 26 0.000 1.0080 ; qtot -1.000
>>>>>> 27 CTL2 1 SDS C8 27 0.000 12.0110 ; qtot -1.180
>>>>>> .
>>>>>> .
>>>>>> 42 HAL3 1 SDS H123 42 0.000 1.0080 ; qtot -1.000
>>>>>> 43 SOD 2 SDS SOD 43 0.000 22.9898 ; qtot 1.000
>>>>>> .
>>>>>>
>>>>>> However I get this warning during the simulation :
>>>>>>
>>>>>> WARNING: Listed nonbonded interaction between particles 25 and 43
>>>>>> at distance 2.303 which is larger than the table limit 2.200 nm.
>>>>>>
>>>>>> Do you have any idea how could I get rid off this warning?
>>>>>>
>>>>>
>>>>> This is a generic simulation failure message, indicating that your system is blowing up. This could be due to any number of reasons, but without more details it's pointless to guess.
>>>>>
>>>>>> Also does the hacked .top file seem correct?
>>>>>>
>>>>>
>>>>> Decoupling the Na+ ion will mean your resulting dG value includes the hydration free energy of Na+, which it doesn't sound like you're interested in.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
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>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> <mailto:jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>> | (410) 706-7441
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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> Gromacs Users mailing list
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