Thanks very much for the information. You are absolutely right, the thing is that I have to remove (manually) all the folders and reconfigure and re-make it. I did not do it , I was using the non-parallel version with mpirun, that causes the error.
I am just curious why they donot specify the prefix for the installation path (like many of the other open source software), and separate the configuration and the final installation files….or, am I missing that?
And, is there any c version of charmm? the install.com seems have tons of issues regarding the machine types... Because, even I finally put the charmm into the old machine as parallel version, I have at least three other types of machines to install later version charmm, frankly speaking, I am terrified for these tasks cause there will be so many "tips" and "hints" and "tricks" which I have no idea ... Just hope it will not drive me into complete nut.
But again, thanks so much for the information. I just hope later on there will be less such “tips”, “hints” or “tricks”. It is REALLY very bad for whoever want to use this software, not mentioning to pay for it, maybe I shall not comment on it, cause it is free already –sort of—for researchers. But, if I were Karplus, I will just hire a bunch of c programmer to re-write the whole thing instead of keep adding patches into it and release endless documentations.