[gmx-users] Charge grps and cut-off

[Sai Pooja]

Hi,


So if I use PME for coloumb interactions, then what are my options?

Would you then suggest breaking up the 12-atom charge grp in the arginine
residue into 2 charge groups?

Would it be enough to make the changes in the .rtp or parameters in other
files must be changed?

POoja

On Sat, Jul 17, 2010 at 11:16 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sai Pooja wrote:
>
>> A charge grp consisting of 12 atoms is created from Arginine residues in
>> my topology file.
>> ; residue  14 ARG rtp ARG  q +1.0
>>   476        NH1     14    ARG      N    150      -0.47     14.007   ;
>> qtot -3.47
>>   477          H     14    ARG     HN    150       0.31      1.008   ;
>> qtot -3.16
>>   478        CT1     14    ARG     CA    150       0.07     12.011   ;
>> qtot -3.09
>>   479         HB     14    ARG     HA    150       0.09      1.008   ;
>> qtot -3       480        CT2     14    ARG     CB    151      -0.18
>> 12.011   ; qtot -3.18    481         HA     14    ARG    HB1    151
>> 0.09      1.008   ; qtot -3.09
>>   482         HA     14    ARG    HB2    151       0.09      1.008   ;
>> qtot -3      483        CT2     14    ARG     CG    152      -0.18
>> 12.011   ; qtot -3.18    484         HA     14    ARG    HG1    152
>> 0.09      1.008   ; qtot -3.09    485         HA     14    ARG    HG2    152
>>       0.09      1.008   ; qtot -3       486        CT2     14    ARG     CD
>>    153        0.2     12.011   ; qtot -2.8     487         HA     14    ARG
>>    HD1    153       0.09      1.008   ; qtot -2.71
>>   488         HA     14    ARG    HD2    153       0.09      1.008   ;
>> qtot -2.62
>>   489        NC2     14    ARG     NE    153       -0.7     14.007   ;
>> qtot -3.32
>>   490         HC     14    ARG     HE    153       0.44      1.008   ;
>> qtot -2.88
>>   491          C     14    ARG     CZ    153       0.64     12.011   ;
>> qtot -2.24
>>   492        NC2     14    ARG    NH1    153       -0.8     14.007   ;
>> qtot -3.04
>>   493         HC     14    ARG   HH11    153       0.46      1.008   ;
>> qtot -2.58
>>   494         HC     14    ARG   HH12    153       0.46      1.008   ;
>> qtot -2.12
>>   495        NC2     14    ARG    NH2    153       -0.8     14.007   ;
>> qtot -2.92
>>   496         HC     14    ARG   HH21    153       0.46      1.008   ;
>> qtot -2.46
>>   497         HC     14    ARG   HH22    153       0.46      1.008   ;
>> qtot -2      498          C     14    ARG      C    154       0.51
>> 12.011   ; qtot -1.49
>>   499          O     14    ARG      O    154      -0.51     15.999   ;
>> qtot -2
>> See charge group 153. It has 12 atoms. This is true for all Arginine
>> residues. It seems that charge groups must have an integer net-charge. As
>> you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge
>> becomes an integer.
>>
>>
>
> Strictly speaking, charge groups do not always have to have a net charge,
> but generally they do.
>
>
>  One option would be to manually make them. In this case, I could simply
>> breakdown this particular charge grp into 2 smaller chargegrps but I am sure
>> if that would be consistent with the forcefield and not sure if it would be
>> possible to set the net charge to an integral value to an integer for the
>> smaller charge groups.
>>
>
> Simply breaking the charge group apart seems too arbitrary.  If you're not
> using PME (which you're not), then you need integral charge groups, so it
> looks like this one has to stay intact.  It just seems like there's the
> potential for inaccurate short-range interactions when the entire sidechain
> is encompassed by a single charge group.  Perhaps for your case it will not
> matter so much; maybe someone else can comment.  There are numerous threads
> in the list archive discussing this situation, so I won't repeat all of that
> here.
>
>
>  Also, is there an alternate way by changing the Cut-off?
>>
>>
> Not really.  Any cutoff you choose might be affected by artifacts of a
> large charge group.
>
> -Justin
>
>  Any thoughts?
>> Pooja
>>
>>
>>
>> Pooja
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
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