[gmx-users] Re: about make_hole

[Graham Smith]

Hi - 

Whoops, the problem with grompp is because I have made a mistake 
in the tutorial that I distributed with make_hole : I meant 

 grompp -f run.mdp -o insert.tpr -c outbilayer.pdb -r outbilayer.pdb
-p ...

(i.e. -o not -s ). The double argument is OK, you are telling it you
want to apply restraints and to use the atoms' original positions as
the reference points for these.

If I understand your mails correctly, the coordinate file that you are
going
to use (popc + water + a cylindrical hole) is popc_b4em.gro;
Since you have added water with genbox you need to minimize it first; 

 something like 
 grompp -f minim.mdp -o min.tpr -c  popc_b4em.gro -r popc_b4em.gro \
 -p popc.top

 ("minim.mdp" is a minimizing file, containing options like the one
you posted)

 mdrun -s min.tpr -deffnm popc_b4em_min 

 Then that should give you a minimized file popc_b4em_min.gro; then do 

 grompp -f run.mdp -o insert.tpr -c popc_b4em_min.gro -r \
   popc_b4em-min.gro -p popc.top

 ("run.mdp" is a MD file, so in it you would have 
  integrator          =  md 
 amongst other things ... see the other tutorials and the manual). 
 
 then 

  mdrun -v -hole -holep hp.mdp -deffnm insert 

  will work, I hope - deffnm sets all input and output file names to 
  insert.[something]. When I wrote "...",  I was trying to imply that
  all   the other normal options to mdrun could be used. 

 
My tutorial is (I now realize) not totally stand-alone; you need to
have some experience of gromacs first, so you will know what I mean
when I imply something rather than spelling it out (or when I make
stupid mistakes!) As David says, it would probably be a good idea to
run a few "normal" simulations first, e.g. share/tutor/speptide. 

Really sorry to have caused you problems, 

Graham 


########################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr