[gmx-users] non zero charge in topolgy

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/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 
proteins.

<snip>

> define              =  -DFLEX_SPC

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

<snip>

>      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

-- 
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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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