[gmx-users] cgnr in top file

[Justin A. Lemkul]

Erik Marklund wrote:
> True. I guess gromacs groups together the terminal hydrogens, overriding 
> the original force field parameters. Can't say why that decision was 
> made, but it will influence your simulation very little.

I think there was a bug report some time ago involving virtual sites on the 
termini of all-atom force fields causing a crash when the terminus crossed a 
periodic boundary.  Could be related to that, although I can't remember the 
exact progress behind the fix.

-Justin

> 
> Erik
> 
> leila karami skrev:
>> Dear Erik
>>  
>> you said Amber03 was not parameterized with charge groups and last 
>> column in your rtp entry holds the chargegroup numbers. but
>> cgnr column in my top file does not looks just like it. in case of H1, 
>> H2 and H3.
>>  
>> /     H1    amber99_17   0.16420     2
>> //     H2    amber99_17   0.16420     3
>> //     H3    amber99_17   0.16420     4
>> //    // /. that's ok. but why
>>  
>> /and my top file is as follow :
>> //  //                                                        //    
>> nr       type          resnr  residue  atom   cgnr   charge     mass  
>> //      //2 amber99_17      1   NGLY     H1      2     0.1642      
>> 1.008  //      3 amber99_17      1   NGLY     H2      2     
>> 0.1642      1.008  //      4 amber99_17      1   NGLY     H3      
>> 2     0.1642      1.008   //   /
>> thanks for your attention        
> 
> 

-- 
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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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