Re: [AMBER] convergence of Ref energies in cpHMD

From: Cruzeiro,Vinicius Wilian D <>
Date: Mon, 20 Jan 2020 20:15:54 +0000

Hello Kolattukudy,

There are some optional flags in that should help you with that. May you copy the exact command you are using and the output is printing so I can give you a suggestion?


Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633<tel:+1(352)846-1633>

On Jan 20, 2020, at 10:44 AM, Kolattukudy P. Santo <<>> wrote:

[External Email]

I am trying to run cpHMD for a non-standard molecule. I find it hard for to converge and the fraction of protonation % is very
fluctuating (1 million equillibration steps) . My residue is pretty large
( about 120 atoms ) as it is a side chain of a carbohydrate polymer
Any strategy for fast convergence ?

*Dr. Kolattukudy P. Santo*
*Post doctoral Associate *
*Department of Chemical and Biochemical Engineering*
*Rutgers, The State University of New Jersey*
*New Brunswick, New jersey*
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Received on Mon Jan 20 2020 - 12:30:01 PST
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