About "equilibrate.conf' of FEP tutorial

From: Aurum Bai (javacfish_at_yahoo.com.cn)
Date: Sat Feb 20 2010 - 07:15:58 CST

Dear everyone,

I want to ask the question about the "equilibrate" of FEP/TI tutorial (01.ethane-ethane).

1. I have done the minimze simulation, then follow ""namd2 equilibrate.conf"" ,but some err happen:

"TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: lambda2
ERROR: lambda
ERROR: fepEquilSteps
ERROR: fepOutFreq
ERROR: fepOutFile
ERROR: fepCol
ERROR: fepFile
ERROR: fep

I try to add "source fep.tcl" or modify some parameters, that is not useful.

So When I equilibrate the system, I delete the "FEP option", then it could run. My file is attchment. Is it right? Or when we do
equilibrate simulation, need we add the parameters of "FEP"?

2. Another question, Can "FEP Cacluation" compute hiding one group and showing this group in another molecule at one system (just like tranfer one group to another molecule)?

Thank you very much!


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