[gmx-users] mdrun_hole problem

[alokjain at iitk.ac.in]

Thanks Florian,
               As you have replied, Yes I had activated logging (that
means I had the molsurf_log option in "for_hole.mdp" file .
But it is not creating my specified log file and also the
normal *.log file in run.mdp file)

As you had suggested I just tried with
nstlog                = 1 (previously it was 100)
nstenergy             = 1

But still it is not printing any energy values in log file,even for zeros
step.

It is creating *.log   *.edr files but not *.trr file, but in the *.edr
file nothing is there.

Can you suggest me , how I can overcome this problem?

Best regards,
Alok


> hi,
>
> On Friday 01 September 2006 17:16, alokjain at iitk.ac.in 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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