[gmx-users] problem in gromacs installation

Manik Mayur manik.mayur at gmail.com
Fri Feb 20 13:02:09 CET 2009

On Fri, Feb 20, 2009 at 2:45 PM, nitu sharma <sharmanitu35 at gmail.com> wrote:

> Dear All,
>                     I have successfully insstalled gromacs on my 32 bit
> i686 linux system but when I give the mdrun command for running gromacs  on
> my system the output is  like this
> "mdrun: error while loading shared libraries:
> /usr/local/gromacs/lib/libmd.so.5: cannot restore segment prot after reloc:
> Permission denied."

This is most likely due to SElinux policies. Since you haven't mentioned the
build of linux you are using, you can try the following:

 - As root, change "#setenforce 0" in ''/etc/selinux/config'' and reboot.

However, if you are using Fedora, go to Administration->Security Level and
Firewall. There, in the SELinux Tab, go to Compatibility and enable the
checkbox for "Allow the use of shared libraries with Text Relocation". Then
click ok.

could you please let me know what exactly the problem is in my installtion
> and what is the solution of this problem.
> Thank you very much for taking out your time for my consideration.
> Nitu Sharma
> Structural biology lab
> School of life Sciences
> Jawaherlal Nehru University
> New Delhi, India.
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Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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