Deal all,
I have already asked a few questions and got patient answers, thank you very much. But I encounter new problems when doing membrane protein simulation. I followed the tutorial (
http://ambermd.org/tutorials/advanced/tutorial16/index.html) to build the box with the command:
"set POPC box { 63.180 63.436 140.466 }
saveamberparm POPC popc.prmotp popc.inpcrd
Ħħ
There is a contradiction between the tutorial and the manual here, because the tutorial mentions that the "set box" will build a periodic box, while the manual says that the "set box" only builds a box. But the manual does not mention what commands can add a specific periodic box. The command solvateoct/solvatebox is not suitable for membrane proteins.
Therefore, I can only use the "set box" command to add a box to the established membrane-water system. At present, the system has been able to run, but in the production run, I have encountered problems, as follows:
"ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values.
Your system density has likely changed by a large amount, probably from starting the simulation from a structure a long way from equilibrium"
It looks like the system ran out of the box. How should this problem be solved?
Thanks!
Qiao Xue
xmgign.126.com
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Received on Tue Jun 18 2019 - 00:00:01 PDT
