From: Ceren Ciraci (cerenciraci_at_gmail.com)
Date: Tue May 26 2020 - 13:33:09 CDT
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
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