[gmx-users] non zero charge in topolgy

Justin A. Lemkul jalemkul at vt.edu
Tue May 11 05:24:44 CEST 2010

Moeed wrote:
> Dear experts,
> 1- I am trying to produce tpr file for EM (there is one hexane molecule 
> in my system). It seems top file has non zero charge. could you please 
> help me how to deal with this problem.

You have the wrong sign on the charge of C3.

> 2-To run the simulation for one single hexane molecule what should the 
> box size be? it is- box  3 3 3 -angles 90 90 90 now!

Box dimensions are determined by the size of the molecule(s) in the system, 
cutoffs used, and the minimum image convention.


> 3- Also in the top file (generated by pdb2gmx) the molecules name that 
> automatically appears is "protein". I dont have water molecule in my 
> sys. Can I change the name of the molecule and remove water topology by 
> hand? I dont know why water topoly is included....

These are all default behaviors of pdb2gmx.  If you have unnecessary #include 
statements (water, ions, etc) you can delete these lines with no ill effect.  As 
for the "Protein" name, you can re-name the molecule however you like, but 
again, this is just the default behavior, since pdb2gmx typically deals with 


> define              =  -DFLEX_SPC

This define statement is completely irrelevant if you're not dealing with water.


>      8   opls_158      1    HEX     C3      3       0.12     12.011   ; 
> qtot 0.12
>      9   opls_140      1    HEX    H31      3       0.06      1.008   ; 
> qtot 0.18
>     10   opls_140      1    HEX    H32      3       0.06      1.008   ; 
> qtot 0.24

Here's where your problem starts.  Note that the charge is no longer zero at the 
end of this charge group.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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