[gmx-users] simulating two peptides in a box

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 7 19:50:01 CEST 2008

Several questions come to mind, aside from trying to sift through your 
interpretation of error messages.  Hint: always show your exact command, 
followed by the relevant portion of the screen output; that way we don't 
have to guess what you've been up to :-)

1. Do you have two different proteins, or are they the same?  If they 
are different, changing the number of Protein molecules in your topology 
will not be correct.  If they are the same, this is fine.

2. Does the order of your topology follow the order of the coordinate 
file?  When you get warnings about non-matching atom names, you should 
be alert that something has gone wrong.


kartik mehra wrote:
> Dear GMX Users,
> I am trying to set up a simulation box with two proteins. I have 
> perused the archives about the methodology of doing so. I tried the 
> recommended option of changing the number of protein molecules in the 
> topology file to 2. However when I run grompp after editconf and 
> genbox, I get warning that the number of co -ordinates do not match 
> (since I had not updated the number of solvent molecules ...) After 
> updating the number of solvent molecules, when I try running grompp 
> again, it shows a warning that the 23644 atom names do not match in 
> top and gro files and that atom names from top files are being chosen .
> Upon subsequent mdrun, the system explodes after a 1-4 interaction 
> warning.
> I was wondering whether anyone could help me out on this ... I do 
> understand that the topic has been discussed pretty often but would 
> appreciate any help ...
> Cheers
> Kartik
> PS: I have not yet tried the other suggestion of translation and 
> rotation followed by concatenating the two files
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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