VMD

Observe water molecules that close to LIG(lipid):

all and within 5 of resname LIG

display resize 800 600

output dcd trajectory

set s1 [atomselect top all]

animate write dcd tmp.dcd waitfor all $s1

exiCATDCD: http://www.ks.uiuc.edu/Development/MDTools/catdcd/ extract certain frames from a trajectory: catdcd -o output.dcd -first ??? -last ??? input.dcd
Here is one website that have many vmd applications: http://hi.baidu.com/sobereva/item/c23f2edeba7400312b35c7dd

 

cp vmd-1.9.2.src.tar.gz ../softwares/
746 cd ..
747 ls
748 cd softwares/
749 ls
750 tar -xvzf vmd-1.9.2.src.tar.gz
751 ls
752 cd vmd-1.9.2/
753 ls
754 vi README
755 vi configure
756 ./configure
757 ls
758 clear
759 ll
760 cd ..
761 ls:
762 cd plugins/
763 ls
764 make LINUXAMD64
765 yum search netcdf
766 sudo yum install netcdf
767 sudo yum install netcdf-devel.x86_64
768 clear
769 history
770 make LINUXAMD64
771 make ARCH=LINUXAMD64 PLUGINDIR=/home/zwei/softwares/plugins distrib
772 pwd
773 gmake distrib
774 sudo gmake distrib
775 cd ..
776 ls
777 cd vmd-1.9.2/
778 ls
779 make clean
780 make veryclean
781 cd ..
782 ls
783 export PREFIX=/home/zwei/softwares/vmd_1.9.2
784 export PLUGINDIR=${PREFIX}/plugins
785 mkdir -p $PLUGINDIR
786 cd vmd-1.9.2/
787 export SRCDIR=$(pwd)
788 echo $SRCDIR
789 cd ..
790 ls
791 cd plugins/
792 ls
793 module load netcdf/gcc
794 make LINUXAMD64 >& Make.linuxamd64.out &
795 jobs
796 ll
797 ll -trh
798 vi Make.linuxamd64.out
799 ll -trh
800 make LINUXAMD64
801 make distrib >&Make.distrib.out &
802 jobs
803 ll -trh
804 vi Make.distrib.out
805 history
806 echo $PLUGINDIR
807 pwd
808 cd ..
809 ls
810 cd vmd-1.9.2/
811 ls
812 export VMDINSTALLBINDIR=${PREFIX}/bin
813 export VMDINSTALLLIBRARYDIR=${PREFIX}/lib
814 echo $PLUGINDIR
815 ln -s $PLUGINDIR .
816 ll
817 ./configure LINUXAMD64
818 cd src/
819 ls
820 make
821 make install

display atom selected:

mol delrep 0 top

set selection1 [atomselect $molid "water within 5 of name MG or water within 5 of name 'Cl-' or water within 5 of name AL or water within 5 of name 'Na+'"]

mol selection "[$selection1 text]"

mol addrep top

 

http://blog.sciencenet.cn/blog-355217-657665.html