From genion -h:
"genion replaces solvent molecules by monoatomic ions at the position of the
first atoms with the most favorable electrostatic potential or at random."
That would explain how genion works, and what you must do to update the topology
correctly. If you have added 2 NA+, then you have also removed 2 SOL.
-Justin
Chitrita Dutta Roy wrote:
What exactly Do we need to change in the topology file suppose if we add
2 NA+ ions in the system..???
On Thu, Dec 18, 2008 at 1:45 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Chitrita Dutta Roy wrote:
Can anyone give me a detailed notes on how to install gromacs 4
with mpi feature..I am using Intel Q9300 and fedora 10.It's very
urgent as i am new to using gromacs plz give me as detailed note
as possible..
Installation instructions are on the Gromacs webpage and the wiki
site (including a heading called "Using MPI").
And after adding some ions using genion when i try to run grompp
again before final mdrun i get some error telling mismatches in
.top and .gro file in some atoms although i have changed the top
files as normally we should adding the ions and changing the
total number of solvents accordingly..Why is it happening Can
anybody help..plzz??
Then you haven't updated your topology correctly. Without seeing
your command line and the output, it's hard to say much more. The
wiki site (again) is your friend here.
-Justin
Thanks.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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