Re: [gmx-users] Restart energy minimization with step .pdb files
Ok, thank you for the clarification; I thought those files where generated no
matter what.
By the way, I am not trying to restart because the simulation crashed: it's
just that I am running on a cluster and the job exceded the prescibed time
limit. The minimimization itself seems to work fine (at least this is what I
can see from ener.edr).
Cheers,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 27 February 2020 13:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Restart energy minimization with step .pdb files
On 2/27/20 4:37 AM, Michele Pellegrino wrote:
> Hi,
>
>
> I am trying to restart steepest descent using the .pdb files generated by
> mdrun. The name of these files has the following pattern:
>
> step#%_n*.pdb
>
> being # and * integers and % a character ('a', 'b' or 'c').
>
> I read the documentation, but I can't understand what those files represent.
>
> Could anyone give me some hint?
step*.pdb files are the coordinates in each spatial domain in an attempt
to help you debug what is going on. I have never been able to employ
them in any useful way. All they really indicate is that your mdrun
process is going to crash due to instability.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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Re: [gmx-users] Restart energy minimization with step .pdb files
On 2/27/20 4:37 AM, Michele Pellegrino wrote:
Hi,
I am trying to restart steepest descent using the .pdb files generated by
mdrun. The name of these files has the following pattern:
step#%_n*.pdb
being # and * integers and % a character ('a', 'b' or 'c').
I read the documentation, but I can't understand what those files represent.
Could anyone give me some hint?
step*.pdb files are the coordinates in each spatial domain in an attempt
to help you debug what is going on. I have never been able to employ
them in any useful way. All they really indicate is that your mdrun
process is going to crash due to instability.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
--
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* Please search the archive at
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Re: [gmx-users] Restart energy minimization with step .pdb files
I am sorry, but I don't fully understand your answer: do you mean step_XXX.pdb
files are generated when atoms are overlapping?
In any case I still do not get the meaning of the labels; what 'a', 'b' and 'c'
stand for?
Thank you for your quick response.
Cheers,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Quyen V. Vu
Sent: 27 February 2020 11:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Restart energy minimization with step .pdb files
It usually happens when you have two or more atoms overlap.
step_XXX.pdb is the lowest energy state that steepest descend can give you
with your input file.
In my opinion, you should look into the log file of energy minimization
step, find out which atom is exerted the maximum force, visualize your
initial input and check is there any atom overlaps with that atom.
Best,
On Thu, Feb 27, 2020 at 10:37 AM Michele Pellegrino wrote:
> Hi,
>
>
> I am trying to restart steepest descent using the .pdb files generated by
> mdrun. The name of these files has the following pattern:
>
> step#%_n*.pdb
>
> being # and * integers and % a character ('a', 'b' or 'c').
>
> I read the documentation, but I can't understand what those files
> represent.
>
> Could anyone give me some hint?
>
>
> Cheers,
>
> Michele
>
>
> p.s. I am running GROMACS 2019.5
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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Re: [gmx-users] Restart energy minimization with step .pdb files
It usually happens when you have two or more atoms overlap.
step_XXX.pdb is the lowest energy state that steepest descend can give you
with your input file.
In my opinion, you should look into the log file of energy minimization
step, find out which atom is exerted the maximum force, visualize your
initial input and check is there any atom overlaps with that atom.
Best,
On Thu, Feb 27, 2020 at 10:37 AM Michele Pellegrino wrote:
> Hi,
>
>
> I am trying to restart steepest descent using the .pdb files generated by
> mdrun. The name of these files has the following pattern:
>
> step#%_n*.pdb
>
> being # and * integers and % a character ('a', 'b' or 'c').
>
> I read the documentation, but I can't understand what those files
> represent.
>
> Could anyone give me some hint?
>
>
> Cheers,
>
> Michele
>
>
> p.s. I am running GROMACS 2019.5
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Restart energy minimization with step .pdb files
Hi,
I am trying to restart steepest descent using the .pdb files generated by
mdrun. The name of these files has the following pattern:
step#%_n*.pdb
being # and * integers and % a character ('a', 'b' or 'c').
I read the documentation, but I can't understand what those files represent.
Could anyone give me some hint?
Cheers,
Michele
p.s. I am running GROMACS 2019.5
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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