[gmx-users] Questions about free energy calculation tutorial

[Justin Lemkul]

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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