Re: About "equilibrate.conf' of FEP tutorial

From: Jérôme Hénin (
Date: Sat Feb 20 2010 - 10:36:43 CST

Dear Aurum,

On 20 February 2010 05:15, Aurum Bai <> wrote:
> 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

This happens because the keywords have changed since the tutorial was
written. The tutorial is being updated. In the meantime, you should be
able to update the FEP script yourself based on the current user's

> 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)?

Certainly. You just have to define a dual topology where modifications
happen at two sites, A->B at one site and B->A at the other. To the
FEP code, it just looks like one transformation.


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