Javier Cerezo wrote:
Hi Tom
This warning comes from a check that (I think) was not present in 4.0.7
version. This problem is usually a consequence of bad charge group
numbering in your topology. Please, provided your topology file and
grompp command arguments.
It is also possible that the charge group is split across PBC, causing it to be
broken. In this case, nothing is wrong. Using a plain cutoff, however,
generally is very wrong...
-Justin
Cheers
Javier
El 11/06/11 05:59, Tom escribió:
Dear Gromacs Users,
My file has no problem when i grompp with verison of 4.0.7
When i swith to Gromacs 4.5.3 and grompp my file, it gives this reports:
----------------------------------------------------------------
NOTE 3 [file grompp.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
Largest charge group radii for Van der Waals: 4.986, 4.983 nm
Largest charge group radii for Coulomb: 6.719, 6.712 nm
WARNING 1 [file grompp.mdp]:
The sum of the two largest charge group radii (13.430987) is larger
than
rlist (1.200000)
-----------------------------------------------------------------------------------
Is there anyone who can help see why different version mak such
problem? How to solve the problem?
Thanks a lot!
Tom
--
========================================
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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