Hi,
It would help to have some more details. What is the architecture of
the computer you are running on? How was cpptraj/Amber compiled (i.e.
what compilers, what options given to cmake, etc). What was the exact
input given to cpptraj, and if possible attach the output from
cpptraj. Thanks,
-Dan
On Fri, Dec 1, 2023 at 4:24 AM Rimóczi Aliz via AMBER <amber.ambermd.org> wrote:
>
> Dear All,
>
> I am writing in connection with a problem which I have recently faced using Amber22. Me and my colleagues are users (not superusers) on the newest supercomputer in Hungary named 'Komondor', we are using the program on this computer. I wanted to use the 'ccptraj' module for stripping solvent molecules. Using parm, parmstrip and parmwrite out commands I did not get the proper output (box_strip.prmtop) from my input (box.prmtop) however I got a message that everything went fine, the stripping is finished and no problems occured. The box_strip.prmtop does not appear in the folder I was working in, not even when I apply a direct pathway. I tried to use trajin, trajout, outparm commands unsuccesfully, nothing has changed.
> Is this problem in connection with the settings of the supercomputer itself or the Amber22? I executed stripping succesfully on a daily basis with Amber16 on another supercomputer, so I find this case very unusual. Can you give me some tips about the possible sources of the problem? If the supercomputer's settings are probably not fine, I will forward your recommendations to the maintainers of Komondor with your permission.
>
> Thank you for your help!
>
> Sincerely,
>
>
> Aliz Rimóczi
>
>
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Received on Fri Dec 01 2023 - 08:00:02 PST
