On 2/26/13 2:06 PM, francesco oteri wrote:
I downloaded and installed gromacs-4.6
but I get the warning
WARNING 1 [file NVE.mdp]:
The sum of the two largest charge group radii (0.067845) is larger than
rlist (1.200000) - rvdw (1.200000)
I attacch the files you may need to solve the problem
NVE.mdp <https://docs.google.com/file/d/0B1ktZ-u2OHFAdUl6UkFJajNGcGs/edit>
processed.top<https://docs.google.com/file/d/0B1ktZ-u2OHFAcG82WnltVmdFN1U/edit>
01em.gro <https://docs.google.com/file/d/0B1ktZ-u2OHFAZ0d3WGs3U1dBaU0/edit>
index.ndx<https://docs.google.com/file/d/0B1ktZ-u2OHFAemxNc0c5YlRlNlE/edit>
Perhaps the previously fixed issue isn't perfect, but again this is the same
symptom where apparently rlistlong is not being fully interpreted. There should
be nothing wrong if you have an adequate setting for rlistlong.
-Justin
2013/2/26 francesco oteri <[email protected]>
Thank you so much for the help!
2013/2/26 Justin Lemkul <[email protected]>
On 2/26/13 12:01 PM, francesco oteri wrote:
I am using 4.5.5...Is it OK?
If it's giving a note about that, then clearly not. Try 4.6. But as I
said, there's nothing actually wrong.
-Justin
2013/2/26 Justin Lemkul <[email protected]>
On 2/26/13 11:47 AM, francesco oteri wrote:
Thank you Justin,
I added
rlistlong = 1.4
but still grompp complains:
NOTE 1 [file 02md.mdp]:
For energy conservation with switch/shift potentials, rlist should
be
0.1
to 0.3 nm larger than rvdw.
Why doesn't grompp looks for rlistlong value?
There was a problem with an older version of Gromacs (I can't remember
which) where grompp ignored rlistlong. It has no implication for mdrun
and
is solved by using the newest version.
-Justin
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==============================**==========
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Cordiali saluti, Dr.Oteri Francesco
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========================================
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
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