Re: error: minimizer slowly moving xxx atoms with bad contacts downhill

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue May 26 2020 - 15:16:08 CDT

Hi Ceren, overlapping atoms => infinite forces.

On Tue, May 26, 2020 at 2:35 PM Ceren Ciraci <cerenciraci_at_gmail.com> wrote:

> I made NAMD wrote the ievery ntermediate step into the *.dcd file but when
> I uploaded the *.dcd file for the first 7 steps, there was no motion of any
> molecule. Besides, the *.out file has the following lines at the last step
> (Step#7) as given below. I will appreciate any help figure out the reason
> for such a crash.
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 7
>
> MINIMIZER SLOWLY MOVING 32 ATOMS WITH BAD CONTACTS DOWNHILL
>
> WRITING COORDINATES TO DCD FILE 3B5H_2nvt.dcd AT STEP 7
>
> WRITING COORDINATES TO RESTART FILE AT STEP 7
>
> FINISHED WRITING RESTART COORDINATES
>
> The last position output (seq=7) takes 0.880 seconds, 1096.137 MB of
> memory in use
>
> WRITING VELOCITIES TO RESTART FILE AT STEP 7
>
> FINISHED WRITING RESTART VELOCITIES
>
> ENERGY: 8 87616.0455 -nan(ind) nan
> nan -981658.7026 99999999999.9999 0.0000
> 0.0000 0.0000 -nan(ind) 0.0000
> -nan(ind) -nan(ind) 0.0000 -nan(ind)
> -nan(ind) 2994776.0857 -nan(ind) -nan(ind)
>
> On Tue, May 26, 2020 at 6:51 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi, as you probably deduced, the minimizer is having a difficult time
>> handling the configuration that you set. It would help others help you if
>> you could provide details on what you tried. For example, have you tried
>> writing the coordinates to a DCD trajectory file often enough and
>> visualizing it?
>>
>> Giacomo
>>
>> On Tue, May 26, 2020 at 11:48 AM Ceren Ciraci <cerenciraci_at_gmail.com>
>> wrote:
>>
>>> I use NAMD software for a project. Our run constantly crashes with the
>>> following message:
>>>
>>> "minimizer slowly moving xxx atoms with bad contacts downhill"
>>>
>>> Could you possibly suggest any troubleshooting tips? We have tried so
>>> hard but haven't been able to come up with a solution yet.
>>>
>>> We greatly appreciate your response and time.
>>>
>>> Sincerely,
>>> Ceren
>>>
>>> --
>>>
>>> Ceren CIRACI, Ph.D.Doçent | Associate Professor
>>> İstanbul Teknik Üniversitesi | Istanbul Technical University
>>> Moleküler Biyoloji ve Genetik Bölümü | Dept. of Molecular Biology & Genetics
>>> Ayazağa Kampusu, 307 MOBGAM Binasi, Maslak 34469 Istanbul-TR
>>>
>>> T: +90 212 285 7255; F: +90 212 285 7254 ; E: ciracic_at_itu.edu.tr
>>>
>>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Research collaborator, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
> --
>
> Ceren CIRACI, Ph.D.Doçent | Associate Professor
> İstanbul Teknik Üniversitesi | Istanbul Technical University
> Moleküler Biyoloji ve Genetik Bölümü | Dept. of Molecular Biology & Genetics
> Ayazağa Kampusu, 307 MOBGAM Binasi, Maslak 34469 Istanbul-TR
>
> T: +90 212 285 7255; F: +90 212 285 7254 ; E: ciracic_at_itu.edu.tr
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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