Sorry Ali, I can't do your work for you. If this is way over your head, then
either forget it, find a colleague to help
you, or spend some time learning bash and gromacs. I'n not commenting on your
approach, but if you modified
your .gro then you need a new .top file. You can create one.
Chris.
-- original message --
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.
GMXLIB=/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/share/gromacs/top
echo "NE_CZ_NH1_NH2_CB_CG_CD System" |
and another lines ........
Please explain more if it is possible,
--
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