[gmx-users] Normal mode analysis

[Smith, Micholas D.]

Hmmm....

How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply.



===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Katrien Clerx <katrien.clerx at student.kuleuven.be>
Sent: Wednesday, February 26, 2020 7:52 AM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis

Yes I used double precision for everything.



-Katrien







From: Smith, Micholas D.<mailto:smithmd at ornl.gov>
Sent: woensdag 26 februari 2020 13:39
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis



Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build.

-Micholas

===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Katrien Clerx <katrien.clerx at student.kuleuven.be>
Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: [EXTERNAL] [gmx-users] Normal mode analysis

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
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