# error message:
TCL: can't read "temp": no such variable
FATAL ERROR: can't read "temp": no such variable
while executing
"runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp"
(file "0.namd" line 83)
note: line 83 is the last line of config file that i provided completely below:
This is nothing related to NAMD, just TCL which is a standalone scripting language. You command uses a variabel temp, which is never defined. Define it like:
set temp 300
Btw. why do you use: "temperature 0" in your input?
actually at the first config file i want to minimize the structure at 0 (runfepmin) and the second one is related to increasing temperature up to 310 kelvin (runfepmin) and the last one is equilibrium (runfep). is it correct?
by the way, i have renamed to or but i didn't succeed.
You should make yourself familiar with NAMD before attempting FEP. The temperature keyword is a NAMD option to specify the initial temperature and is required if you don't have velocities already (velocities keyword). The runFEP procedure you have has nothing to do with NAMD, its plain TCL commands that utilize NAMDs fep implementation. You copied the command from the tutorial that inlcuded a variable "temp" which you never set. You should also make yourself familiar with TCL.
You can minimize your structure once, then equilibrate without FEP. Then run each lamda step inlcluding a preceeding equilibration to each lamda again (lamdaequilsteps) which is later ignored by the parseFEP plugin in VMD.
I again recommend to start with normal MDs, FEP is hard to do right, even if you know what you are doing.
sure, you are right. because i'm not familiar with tcl code yet.
and i have another question that telated to fep. what's the meaning of fepmin, feplist & runfep?
is it correct to run minimization and then perform equilibrium with runfep command??
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