Re: [AMBER] NVE Energy/Temperature Drift Issue

From: James W. Snyder, Jr. <>
Date: Mon, 1 Jul 2013 21:51:20 -0700 (PDT)


In retrospect, that makes a lot of sense, and I feel a little stupid for missing that. Out of curiosity though, why is nscm=0 necessary?



----- Original Message -----
From: "Ross Walker" <>
To: "AMBER Mailing List" <>
Sent: Monday, July 1, 2013 9:43:06 PM
Subject: Re: [AMBER] NVE Energy/Temperature Drift Issue

Hi Jim,

You need to set cut=999 and nscm=0 for NVE runs. It is not possible to
conserve energy in a non-pme calculation in AMBER with a cut off.

All the best

On 7/1/13 9:40 PM, "James W. Snyder, Jr." <> wrote:

>Yeah, so I am not totally sure how much the energy is drifting because
>there is a lot of noise. The temperature drifts by 60K is 120ps roughly.
> Also, I am using an explicit solvent model/solvation sphere. From what
>I understood, this warranted using ntb=0 and igb=0. If that's not the
>case, please let me know. Also, I don't really want to write the results
>every step. Those comments are residual from when I was debugging
>something. I think dsum_tol = 0.000001 is also from something else, but
>I didn't bother removing it because it has no impact on the calculation.
>----- Original Message -----
>From: "Daniel Roe" <>
>To: "AMBER Mailing List" <>
>Sent: Monday, July 1, 2013 9:17:59 PM
>Subject: Re: [AMBER] NVE Energy/Temperature Drift Issue
>Could you provide some more details? Could you quantify what you mean
>by substantial drift? The options ntb = 0 and since it's not
>explicitly set igb = 0 imply you're running your calculation in vacuum
>- is that correct? If so, your cutoff (16.0) seems really low,
>especially for a 25K atom system - also note that Amber force fields
>were not designed with vacuum calculations in mind, so you should be
>cautious in interpreting your results.
>On Mon, Jul 1, 2013 at 9:35 PM, James W. Snyder, Jr.
><> wrote:
>> ntpr = 1000, !print detials to log every step
>> ntwx = 1000, !write coordinates to mdcrd every step
>> ntwr = 1000, !write restart file every step
>If you really want to be writing this stuff every step (as your
>comments imply) these should be set to 1, although that's really only
>useful for debugging purposes.
>> dsum_tol = 0.000001, ! Increase PME accuracy
>Since you're not using the PME code (ntb = 0) this option has no effect.
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>(801) 587-9652
>(801) 585-9119 (Fax)
>AMBER mailing list
>AMBER mailing list

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Received on Mon Jul 01 2013 - 22:00:06 PDT
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