Why does the water box collapse in an aMD

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Jun 13 2016 - 21:11:00 CDT

• Next message: Jean-François Fabre: "Missing atom type for hydroperoxide"
• Previous message: Josh Vermaas: "Re: Topology Command in VMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear all, 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. Yeping Sun

• Next message: Jean-François Fabre: "Missing atom type for hydroperoxide"
• Previous message: Josh Vermaas: "Re: Topology Command in VMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:15 CST