hi,
On Friday 01 September 2006 17:16, [EMAIL PROTECTED] wrote:
> Dear All,
>
> This question is regarding the modified mdrun program i.e mdrun_hole that
> is used for creating hole in the lipid bilayer to insert a protein into it.
>
> When I am trying to run the following command:
>
> mdrun_hole -v -hole -holep for_hole.mdp -s run.tpr -o run.trr -x run.xtc
> -c after_run.gro -g run.log -e run.edr
>
> though it appears to be running (i.e. even the top command in linux shows
> it to be running) but the log file does not show the energy values and
> stops at the following point:
>
> ####################################################################
> There are 6998 molecules, 16413 charge groups and 34175 atoms
> There are 0 optimized solvent molecules on node 0
> There are 6729 optimized water molecules on node 0
> Will do PME sum in reciprocal space.
>
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
> {A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
> #########################################################################
>
> Also, I have checked the correctness of the tpr file generated by using
> simple gromacsv3.1.4 grompp. i.e. when I issue the following command:
>
> mdrun -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -g run.log -e
> run.edr
>
> then it runs properly.
>
> Is there any way of checking whether the mdrun_hole has been installed
> properly (although when I write "mdrun_hole -h", it prints out the hole
> parameters too, probably telling that mdrun_hole has been installed)?
> Has anybody ever faced a similar kind of problem with mdrun_hole?
> kindly suggest me something.
have you activated logging?
Perhaps set them to
nstlog = 1
nstenergy = 1
So every step get logged if this works you can reduce it to normal ones again.
Does mdrun generate *.trr file edr ..?
>
> waiting for the response,
> regards,
> Alok.
>
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Greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Telephone: +49(0) − 9131 − 85 26581
Mailto: florian.haberl AT chemie.uni-erlangen.de
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