[gmx-users] problem with g_density -center

[Ali Alizadeh]

Dear Chris

I found your topic:

    chris.neale | 21 Aug 01:30   ,   problem with g_density -center

The following text is your email. Is it correct?

I pursue your steps but :

1- I don't understand first commands that related to directories and :

   empty.mdp ?  and  command : avg=($(cat coord.xvg|grep -v '[@|#]' |
awk '{x+=$2;y+=$3;z+=$4;n++}
                                                END{print -1*x/n,-1*y/n}'))

2- I encounter with a problem in now make a new .tpr file, my error:

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

my top file is the same first top file in my simulation,

3- You can help me by simpler commands?

1- rm -rf TEMPORARY_FILES
mkdir -p TEMPORARY_FILES
echo "KSC_DOPC" | trjconv -f bothsides_center_adjusted_*.xtc -o
/dev/shm/tmp.xtc -n cn.ndx

2- 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" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-center -pbc mol -f /dev/shm/tmp.xtc -o /dev/shm/tmp2.xtc -s
../../useful/dry.tpr -n cn.ndx
mv /dev/shm/tmp.xtc TEMPORARY_FILES

3- echo "DOPC System" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-center -pbc atom -f /dev/shm/tmp2.xtc -o /dev/shm/tmp3.xtc -s
../../useful/dry.tpr -n cn.ndx
mv /dev/shm/tmp2.xtc TEMPORARY_FILES

4-  ## now make a new .tpr file in which the solute is at the center of the box
#first output a single frame
echo "NE_CZ_NH1_NH2_CB_CG_CD System" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-f /dev/shm/tmp3.xtc -dump 125000 -o /dev/shm/tmpgro.gro -s
../../useful/dry.tpr -center -pbc mol -n cn.ndx

5- #make a new .tpr file
touch empty.mdp
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/grompp
-p
/project/pomes/cneale/GPC/fromScratch/ARG/MANY_RUNS/TEMPLATE/FILES/complete_dry.top
-c
/dev/shm/tmpgro.gro -f empty.mdp -o centered.tpr -maxwarn
1

6- echo "NE_CZ_NH1_NH2_CB_CG_CD System" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-fit transxy -pbc atom -f /dev/shm/tmp3.xtc -o /dev/shm/tmp4.xtc -s
centered.tpr -n cn.ndx
mv /dev/shm/tmp3.xtc TEMPORARY_FILES

7- echo "System" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-box 6 6 14 -f /dev/shm/tmp4.xtc -o /dev/shm/tmp5.xtc -s centered.tpr
-n cn.ndx
mv /dev/shm/tmp4.xtc TEMPORARY_FILES

8- echo "DOPC System" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-center -pbc none -f /dev/shm/tmp5.xtc -o /dev/shm/tmp6.xtc -s
centered.tpr -n cn.ndx
mv /dev/shm/tmp5.xtc TEMPORARY_FILES

9- echo "NE_CZ_NH1_NH2_CB_CG_CD System" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-fit transxy -pbc none -f /dev/shm/tmp6.xtc -o /dev/shm/tmp7.xtc -s
centered.tpr -n cn.ndx
mv /dev/shm/tmp6.xtc TEMPORARY_FILES

10- # Now center the solute at 0 0 0
echo "NE_CZ_NH1_NH2_CB_CG_CD" |
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/g_traj
-f /dev/shm/tmp7.xtc -ox -s ../../useful/dry.tpr -n cn.ndx -com
avg=($(cat coord.xvg|grep -v '[@|#]' | awk '{x+=$2;y+=$3;z+=$4;n++}
END{print -1*x/n,-1*y/n}'))

11- /project/pomes/cneale/GPC/exe/intel/gromacs-4.5.3_modtrjconv/exec/bin/trjconv
-f /dev/shm/tmp7.xtc -o /dev/shm/tmp8.xtc -trans ${avg[0]} ${avg[1]} 0
mv /dev/shm/tmp7.xtc TEMPORARY_FILES

--
Sincerely


-- 
Sincerely

Ali Alizadeh
University of Tehran
College of engineering(Fanni)
Department of chemical engineering
IPE (Institute of Petroleum Engineering)
M.Sc Candidate, class of 2013
B.Sc Graduate 2011(University of Tehran,Fanni)