[gmx-users] gromacs 4.0 vs 4.5

[Amit Choubey]

Thanks Justin, I can see that there is no problem when i fix the
periodicity.

Amit

On Tue, Jul 19, 2011 at 2:52 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Amit Choubey wrote:
>
>> Hi all,
>>
>> I am doing dppc-water simulation. I am using structure and topologies from
>>
>> http://moose.bio.ucalgary.ca/**index.php?page=Structures_and_**Topologies<http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies>
>>
>> In version 4.0 when i do grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp
>> -p system.top
>>
>> it creates npt.tpr without any errors.
>>
>> Using the same structure and topologies when i issue
>>
>> grompp_v4.5.3 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top
>>
>> it gives out the following warning
>>
>> Largest charge group radii for Van der Waals: 5.354, 5.297 nm
>> Largest charge group radii for Coulomb:       5.354, 5.297 nm
>> WARNING 1 [file npt.mdp]:
>>  The sum of the two largest charge group radii (10.650990) is larger than
>>  rlist (1.200000)
>>
>> I dont think the charge group should be so big. Can someone suggest what
>> is going on ?
>>
>>
> The input file contains broken molecules.  There is nothing wrong, per se,
> but only in the case when molecules are split across periodic boundaries.
>  This is a new check as of version 4.5.
>
> -Justin
>
>  Ami
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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