[gmx-users] Broken protein after EM

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Aug 27 14:27:49 CEST 2012

Dear gmx users,

I'm simulating a protein in water. I ran these commands:
1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic
3.genbox -cp monomer_newbox.gro -cs spc216.gro -o monomer_solv.gro -p topol.top
4.grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr
5.genion -s ions.tpr -o monomer_solv_ions.gro -p topol.top -nname CL -nn 1
6.grompp -f EM.mdp -c monomer_solv_ions.gro -p topol.top -o EM.tpr
7.mdrun -v -deffnm EM

Up to step 7 everything is normal. When I run the 7th command and then visualize the product of EM, the protein is broken into 3 distinct parts. Would you please give me your suggestions to solve?
Is PBC may be the reason of such problem? 

Thanks in advance.

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