Re: [AMBER] Free energy calculation SHAKE's failure when heating.

From: Hannes Loeffler <>
Date: Fri, 24 Feb 2017 16:47:42 +0000

On Fri, 24 Feb 2017 19:11:53 +0300
Artem Shekhovtsov <> wrote:

> Hi! I have a problem with blowing system on relative free energy
> calculation.
> I finished tutorial A9 without problem and decided to try simulate
> some simple system.
> End states of simulation is n-butane and isobutane.
> So I prepared starting files and parametrize molecules in antechamber.
> I want to do main cycles (minimization -> heating -> pressuring ->
> md) at each lambda point of simulation, not only at lambda = 0.5.
> My system blew at "lambda = 0.05 decharge stage"

Ah, right. That can be done with ifsc=0.

Have you tried to minimize at, say, lambda=0.5 and use this structure
to go into heating? Have you had success with any other nearby lambda
and tried to start from that end structure?


AMBER mailing list
Received on Fri Feb 24 2017 - 09:00:04 PST
Custom Search