[gmx-users] About Usage of maxwarn option in EM Afer first first Shrinking

Justin Lemkul jalemkul at vt.edu
Sat Nov 10 20:16:37 CET 2012

On 11/10/12 10:10 AM, vidhya sankar wrote:
> Dear Justin Thank you  For your Previous reply,
>                                                                        For My system        After First Shrinking Using Cut-off Value DPPC  18
> perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
> Then  I do the EM.During EM I need to use -maxwarn 1 option Otherwise I have got Error as follows in  grompp    If i use -maxwarn 1 then it runs Successfully
> May i use this -maxwan  option  in first Shrinking ?

There are very few reasons to use -maxwarn; this is not one of them, as far as I 
can see.

> ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top  -o 2KDQDPPCem.tpr
> Number of degrees of freedom in T-Coupling group rest is 19557.00
> Largest charge group radii for Van der Waals: 1.201, 1.144 nm
> Largest charge group radii for Coulomb:       1.201, 1.144 nm
> WARNING 1 [file emdppc.mdp]:
>    The sum of the two largest charge group radii (2.345197) is larger than
>    rlist (1.200000)

The magnitude of the charge group radii suggests you have broken molecules or 
otherwise unacceptable geometry produced by some previous instability.  This 
warning is discussed in greater detail at 



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


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