biowerkzeug

Hi

Actually I also have played around with the many commands from the mpd including the mpdboot. At the moment there is still no success yet. I hope I am not yet give up to test your program. If you come across to have any suggestion, please advise.

Best regards.

Hi, I've changed to full pathway now. It seemed working because the log.txt files appear in each directory. Now the problem is as before. The log.txt files look ok, no error indication. But, the simulation is not running. Do you need to run mpdboots? or specify any machinefile before running the mpi...

Hi, Regarding the "align principal axis", I 've made some testing for x, y and z axis. The results are: when the input is 2/-2 (y) or 1/+1 (x), the helices will align to normal axis (z-axis). But, when with the input 3/-3, the helices will align to other way, maybe x or y. Thus, for my cas...

Hi It is still not working. I have changed the filenames (the hippo_p3_mpi and also the configfile.dat to configfile. Below is the error msg, after the command > mpiexec -configfile configfile problem with execution of ./hippo_p3_mpi on node002: [Errno 2] No such file or directory problem with execu...

Hi Martin I managed to install the mpich2 in my home cluster. As before, when I run the ./hippo_p3_mpi the log.txt seemed normal but the simulation actually not running at all. Then I tried to follow your suggestion as above: what I did 1. I edit your remc_temperature.dat and configfile.dat to have ...

Hi

I want to study interaction between 2 helices. As an example, I want to put both helices of GpA with 10 A distance to each other. My objective here is to get the helices to come in contact. Do I need to edit any cutoff in the input file?

Thanks

Hi

I just found out that my cluster does not having the MPICH2 installed. Is there any other way to run the REMC? However, I will try to install the MPICH2.

Regards

I am also having the same output as m.kalavera.

Regarding the hippo_input.txt temperature (T), do we need to have the same temperature as in remc_temperature.dat? or which temperature should I put?

Thank you.

Hi Martin

Actually, I only making the test by using the files from the test jobs. I changed the vpu_GBIM input file with the walp_MD input file. In addition with one line of the align principal axis.

Below attached is the hippo_input.txt

Thank you.

Thank you for your quick reply. As my previous mgs, I pasted the error msg from the log.txt. I have tried this paramater of align principal axis in MC, yes it's working. From the movie we will see the movement of the helix. I added this parameter line in MD input file, but the log file gave me the e...