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

[Justin Lemkul]

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 
http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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