From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Jun 13 2016 - 21:11:00 CDT
In order to sample the conformational space of a small local portion in a protein complex, I am trying to do an aMD. I keep the backbone atom of the most resides in the protein (except the residues whose conformations I am studying) fixed. In order to aviod constraint failure, I set the langevinPistonPeriod and langevinPistondecay to 1000 and 500 (10 time of those in a cMD). Strangely, the water molecules in the water box become disperse and the water box collapses shortly after the simunlation begins. This phenomenon seems to have no relation with the "wrapAll" parameter because whether it is set to "on" or "off", the water box collapse occurs.
Do you have some ideas to tackle this problem?
Thanks a lot.
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