[gmx-users] problem with g_density -center

Ali Alizadeh ali.alizadehmojarad at gmail.com
Fri Oct 19 17:24:36 CEST 2012

Dear Chris

I know that these commands are not similar to your code at all.

                        1-  trjconv -f md.xtc -o tmp.xtc -n cn.ndx

                        2- trjconv -center -pbc mol -f tmp.xtc -o
tmp2.xtc -s md.tpr -n cn.ndx tmp.xtc

                        3- trjconv -center -pbc atom -f tmp2.xtc -o
tmp3.xtc -s md.tpr -n cn.ndx tmp2.xtc

      4-  ## now make a new .tpr file in which the solute is at the
center of the box
      #first output a single frame

                           trjconv -f  tmp3.xtc -dump 125000 -o
tmpgro.gro -s md.tpr -center -pbc mol -n cn.ndx

     5- #make a new .tpr file
     touch empty.mdp

                         grompp -p mytop.top -c tmpgro.gro -f
empty.mdp -o centered.tpr -maxwarn 1

At this step give me an error :

     Fatal error:
Invalid line in tmpgro.gro for atom 1:
    1LI      C1    1   0.8   1.9   0.7

I know this error related to my .top file. Because my top file did not
change while my .gro file changed.

2- I really did not find out these line in your commands. I'm not a
professional linux programmer.

echo "NE_CZ_NH1_NH2_CB_CG_CD System" |

and another lines ........

   Please explain more if it is possible,



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