[gmx-users] charge group radii- use maxwarn or increase rlist?

[Justin A. Lemkul]

Moeed wrote:
> Dear experts,
> 
> Please kindly comment on this error. Thank you very much.
> 
> I am getting the known charge group radii error. (in 4.0.7 version with 
> the same settings my simulations run with no error)
> 
> ==========================
> NOTE 1 [file md.mdp]:
>   The sum of the two largest charge group radii (0.205676) is larger than
>   rlist (1.100000) - rvdw (1.000000)
> 
> There was 1 note
> . . .
> 
> turning all bonds into constraints...              
> turning all bonds into constraints...
> Largest charge group radii for Van der Waals: 0.103, 0.103 nm    
> This run will generate roughly 317 Mb of data
> 
> ===================================
> 
> This error has been discussed several times on the archive after release 
> of 4.5.3. Please note that my charge groups are CH3 and CH2 only! . To 
> treat this error I dont know If I need to increase rlist (as suggested 
> in the first link below) or use maxwarn -1 ( second link). How can I 
> diagnose which one to choose?
> 
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/057830.html
> 
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html
> 

In the latter case, the problem was a result of groups being split by PBC.  This 
is not your problem.  Be careful about taking posts out of context.

It's usually better to increase rlist for proper energy conservation.  You 
haven't posted your .mdp file (which is usually pretty important for 
understanding what's going on), but I'll assume you're using some sort of switch 
or shift function for either van der Waals or Coulombic interactions.  In this 
case, the manual is pretty clear about proper use, although you appear to not be 
using any charges at all.  How does that make sense?  What is your objective? 
Even OPLS hydrophobic moieties should have small partial charges across C-H bonds.

-Justin

> ==================================================
> charge groups of solute:
> 
>      1   opls_135      1   EthB     C1      1          0     12.011   ; 
> qtot 0
>      2   opls_140      1   EthB    H11      1          0      1.008   ; 
> qtot 0
>      3   opls_140      1   EthB    H12      1          0      1.008   ; 
> qtot 0
>      4   opls_140      1   EthB    H13      1          0      1.008   ; 
> qtot 0
>      5   opls_136      1   EthB     C2      2          0     12.011   ; 
> qtot 0
>      6   opls_140      1   EthB    H21      2          0      1.008   ; 
> qtot 0
>      7   opls_140      1   EthB    H22      2          0      1.008   ; 
> qtot 0
>      8   opls_136      1   EthB     C3      3          0     12.011   ; 
> qtot 0
>      9   opls_140      1   EthB    H31      3          0      1.008   ; 
> qtot 0
>     10   opls_140      1   EthB    H32      3          0      1.008   ; 
> qtot 0
>     11   opls_136      1   EthB     C4      4          0     12.011   ; 
> qtot 0
>     12   opls_140      1   EthB    H41      4          0      1.008   ; 
> qtot 0
>     13   opls_140      1   EthB    H42      4          0      1.008   ; 
> qtot 0
> 
> ==================================
> 
> Thanks
> moeed
> 

-- 
========================================

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

========================================