[gmx-users] To Mark: cg in vaccum

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 22 13:01:38 CET 2006

nur avneet wrote:
> Dear Mark
> Thanks for your guidance.
> But I am not clear with what you wrote regarding my question:
> is their any particular value of emtol in mdp 
> files of steep and cg, that we should use... I use emtol=1000 in the steep file, and then when i do cg i keep it 100, 50, 10, 8, 2 step by step.

If you read the manual... emtol gives the maximum value for the force on 
an atom for the EM to be considered converged. So the smaller you have 
it, the closer you rate to be to the very bottom of the potential well 
(think about the gradient on a harmonic potential...). There's no 
"right" value - you choose something that suits your end application. As 
I said last time, if you're doing a normal mode analysis, it's worth 
spending some time to get right to the minimum. If you're just preparing 
MD, then it's probably not worth bothering with more than one iterate of 
cg after a steep, since as soon as you heat it, the equipartition 
theorem tells you that you aren't going to stay at the very bottom of a 
well. All you're doing here is fixing gross problems that would lead to 
massive local heating (equipartition again) if you were to just start MD 
with them present.

> Please explain me.
> What value of emtol should i select for cg if this is not correct...(n if not correct then why it is not correct)

I can't answer that - only you can.


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