[gmx-users] Questions about free energy calculation tutorial

Tue Nov 1 12:31:32 CET 2016

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?

Also does the hacked .top file seem correct?

Thanks a lot!

> On 28 Oct 2016, at 17:05, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 10/28/16 4:22 AM, gozde ergin wrote:
>> Thanks Justin,
>> 
>> Actually for my case I’ll put the methane molecule inside cubic box not spherical.
> 
> The geometry of the restraint is what is relevant.  If it's a spherical flat-bottom potential (the easiest thing to use) then you need to account for a spherical restriction.  The cube is periodic, so its shape is irrelevant.
> 
>> There is method called  'Boltzmann exponential reweighting’, however I could not figure out how to apply this method to methane-water system.
>> With the command of g_energy I could get the flat-bottom restraint energy, do you think I just need to remove these energy from the result \DeltaG?
>> I would like to learn if you have any idea and source to suggest.
> 
> It's not just something g_energy can subtract out; you're changing the entropy by a factor related to the volume.  It should be something like -RTln(V/V0) where V0 is the molar volume in the gas phase and V is the volume to which you are restricting the molecule.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 27 Oct 2016, at 20:58, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 10/27/16 11:35 AM, gozde ergin wrote:
>>>> Dear all,
>>>> 
>>>> I follow the Justin’s free energy calculations: Methane in Water tutorial. (Thanks Justin!)
>>>> I would like to ask two questions:
>>>> 
>>>> 1) Is there specific reason to use sd integrator?
>>> 
>>> Langevin dynamics gives better sampling.
>>> 
>>>> 2) Methane molecules is free to sample every x,y,z point in the water bulk.
>>>>   I would like to apply a flat-bottom restraint and keep methane molecule in the centre of bulk.
>>>>   I want to prevent methane movement in z direction.
>>>>   Do you have any idea how to remove the effect of flat-bottom restraint afterwards?
>>>> 
>>> 
>>> You're confining it to a spherical volume, so you need to account for that entropic contribution.
>>> 
>>> -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
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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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