[gmx-users] Questions about free energy calculation tutorial

Thu Nov 3 15:56:20 CET 2016

> 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?

> 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> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
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