[gmx-users] Non-zero charged system

Tivadar Orban t.orban at csuohio.edu
Sun Mar 24 04:42:54 CET 2002


I want to simulate myoglobin witch has a non-zero charge (-1). This was been
detected by grompp.
My question is: 
Should I run grompp and obtain the .tpr as an output, after that run genion
with the .tpr, from grompp, as an input and add 5 Na and 4 Cl and obtain a
.gro output file. 
Then I¹ll need the .tpr file for mdrun (input) with 5 Na and 4 Cl (therefore
zero charge/system).
So should I run x2top (with the .gro and .top from the first steps as a
input files) in order to obtain the zero-charged .tpr as an output and use
this for mdrun? Or there is another aproach?

If a response would require a lot of effort, it¹s ok even if you say that
until this point I¹m on the right way or the wrong one.

Tivadar, Orban  
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