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
Ross
On 7/1/13 9:40 PM, "James W. Snyder, Jr." <jsnyder3.stanford.edu> wrote:
>Hey,
>
>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.
>
>Thanks,
>
>Jim
>
>----- Original Message -----
>From: "Daniel Roe" <daniel.r.roe.gmail.com>
>To: "AMBER Mailing List" <amber.ambermd.org>
>Sent: Monday, July 1, 2013 9:17:59 PM
>Subject: Re: [AMBER] NVE Energy/Temperature Drift Issue
>
>Hi,
>
>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.
><jsnyder3.stanford.edu> 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.
>
>-Dan
>
>--
>-------------------------
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>http://home.chpc.utah.edu/~cheatham/
>(801) 587-9652
>(801) 585-9119 (Fax)
>
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Received on Mon Jul 01 2013 - 22:00:05 PDT
