[gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

>>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?

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
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.