[gmx-users] gromacs installation problem

Hi everyone, I met a problem in the installation of gromacs-4.5. There isn’t any mistake in the configuration step, but in the “make” step, it exit with the error: make[4]: *** No rule to make target `/usr/incluDe/gnu/stubs-64.h', needed by `sgetri.lo'. Stop. make[4]: Leaving directory `/home/md

Re: [gmx-users] The energy minimization....

Mark:Thank you for your reply!I have checked my topology file of the ATP, I think there isn't any problem with it. When I do the grompp (only use the ATP molecule), there is not any warning and error, it stopped at 14th step, and return the following messege:Step=    0, Dmax= 1.0e-02 nm, Epot= -

Re: [gmx-users] The energy minimization....

><[EMAIL PROTECTED]><[EMAIL PROTECTED]>So look at your structures like I said last time! I'm not here to give>my valuable time giving free advice in order to have it ignored...Thank you very much for your kindness and patience. Maybe sometimes my questions seems to be silly and boring, my knowledge

Re: [gmx-users] The energy minimization....

, the coordinates of all atoms are "nan". So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal?Thank you very much!Duan<[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PR

[gmx-users] How to calculate the average distance or energy between two residues?

Hi, everyone!I want to calculate the average energy (like vdw potential) and average distance between two residues (or two atoms) during a simulation process, how can i do this? Is there any exist package?best wishes! ___ gmx-users mailing listgmx-u