amber如何实现续跑

我要吃泡面

请问amber如何实现中断续跑和跑完了设置之后想延长时间的续跑？跑完以后查看RMSD发现没有平衡

rpestana94

You can extend the time using for the second simulation the output of the first one, this is, in the parameters -c and -ref (if you are using this one) you should put the -r of the previous simulation and then you combine the two simulations.

Ex:
*First simulation
sander -i xxx.in -o xxx.out -p xxx.parm7 -c xxx.rst7 -r coord1.rst7 -x cord1.nc

*Continue from the first simulation
sander -i xxx.in -o xxx.out -p xxx.parm7 -c coord1.rst7 -r coord2.rst7 -x cord2.nc

And then in cpptraj:

parm xxx.parm7
trajin cord1.nc
trajin cord2.nc
trajout all_traj.nc

我要吃泡面

thank you for your answer