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
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
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