- gmx pairdist -s md.tpr -f md.xtc -o pairdist.xvg -ref "group \"C-alpha\"" -refgrouping none -sel "group \"C-alpha\"" -selgrouping none
上面指令的參數意思分別是:
- md.tp:configuration file
- md.xtc:trajectory file
- pairdist.xvg :任意兩兩C-alpha原子之間的距離存放在這邊。參考pairdist的說明,如果reference有N群 (r1, r2 ... rN)、selection有M群 (s1, s2 ... sN),那總共就會有1 + N*M個欄位。第一個欄位是時間,後面接的就是距離r1-s1, r2-s1 ... rN-s1 再來是 r1-s2, r2-s2 ... rN-s2、...、r1-sM, r2-sM ... rN-sM
- -ref "group \"C-alpha\"":reference points是C-alpha原子
- -sel "group \"C-alpha\"":比較的對象是C-alpha原子
- -refgrouping none:把reference group拆成一個一個比較
- -selgrouping none:把selection group拆成一個一個比較
若是想要手動選取,參考GROMACS selection語法《Selection syntax and usage》。下面橘色的部分是輸入的指令,黑色是程式會給的回應,紅色是組合鍵:
$ gmx pairdist -s md.tpr -f md.xtc -o pairdist.xvg
...
(Reference positions to calculate distances from):
(one per line, <enter> for status/groups, 'help' for help)
> group "C-alpha" and residue 6
... Specify any number of selections for option 'sel'
(Positions to calculate distances for):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> group "C-alpha" and residue 1
> group "C-alpha" and residue 6
> group "C-alpha" and residue 20
> Ctrl-D
上述指令計算residue 6的C-alpha與其他三個residue 1, 6, 20的C-alpha之間的距離
_EOF_
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