[gmx-users] differences in plot between gromacs and vmd

[Shubhangi Gupta]

Hello,

I have simulated a metalloenzyme, containing zinc, in gromacs for
100 ns. When i plot distance between zinc and a specific atom in protein,
the plots obtained are different in vmd and gromacs (using gmx distance).
vmd shows that the zinc has moved out of the protein at the end of
trajectory, whereas gromacs shows it is intact. How can the differences
between the two be accounted for?
 The plots are linked here.

https://www.dropbox.com/s/pwrpid0lwnewzet/vmd_image.png?dl=0
https://www.dropbox.com/s/1v2hzd1g62ldk4y/vmd_plot.png?dl=0
https://www.dropbox.com/s/b75xdgjlu2urb7y/xmgrace_plot.png?dl=0

Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.

e-mail ID: ignahbuhs.gup...@gmail.com
   shubhangi_gu...@iitb.ac.in



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Re: [gmx-users] What is the difference of using "system" and separating groups for "tc-grps"?

[ZHANG Cheng]

Thank you very much Eric Smoll!


I will use "tc_grps = Protein Non-Protein".




-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Mon, Jan 28, 2019 09:45 AM
To:  "gromacs.org_gmx-users";

Subject:  What is the difference of using "system" and separating groups for 
"tc-grps"?



In the mdp file, I am using "tcoupl = v-rescale". 


Is there a difference between using "system" and separating groups for 
"tc-grps"?


e.g. 
; using "system":
tc-grps  = system 
tau-t= 1.0 
ref-t= 335 



; using separating groups:
tc-grps  = Protein W NA CL
tau-t= 1.0 1.0 1.0 1.0
ref-t= 335 335 335 335



Thank you!
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Re: [gmx-users] Scroll through previous questions

[Eric Smoll]

Hello Neena,

These links should help.

http://www.gromacs.org/Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

The first link seems to suggest that a standard search with a search engine
like Google should scan the Gromacs archive entries.
The second link suggests that you can limit Google search engine results to
the Gromacs archive entries by adding "site:https://mailman-1.sys.kth.se;
in the search bar.

Best,
Eric

On Sun, Jan 27, 2019 at 8:01 PM Neena Susan Eappen <
neena.susaneap...@mail.utoronto.ca> wrote:

> Hi Gromacs users,
>
>
> Is there a quick way to scroll through previous questions in the mailing
> list? Now, I am able to control find my question of interest only for each
> month separately. Can I look through the entire log file from 2000 till now
> at once?
>
>
> Thanks,
>
>
> Neena Eappen
> Graduate Student
> Jockusch Lab, U of T
> --
> Gromacs Users mailing list
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[gmx-users] Scroll through previous questions

[Neena Susan Eappen]

Hi Gromacs users,


Is there a quick way to scroll through previous questions in the mailing list? 
Now, I am able to control find my question of interest only for each month 
separately. Can I look through the entire log file from 2000 till now at once?


Thanks,


Neena Eappen
Graduate Student
Jockusch Lab, U of T
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Re: [gmx-users] What is the difference of using "system" and separating groups for "tc-grps"?

[Eric Smoll]

Hello,

The following link should help.

http://www.gromacs.org/Documentation/Terminology/Thermostats

Best,
Eric

On Sun, Jan 27, 2019 at 6:46 PM ZHANG Cheng <272699...@qq.com> wrote:

> In the mdp file, I am using "tcoupl = v-rescale".
>
>
> Is there a difference between using "system" and separating groups for
> "tc-grps"?
>
>
> e.g.
> ; using "system":
> tc-grps  = system
> tau-t= 1.0
> ref-t= 335
>
>
>
> ; using separating groups:
> tc-grps  = Protein W NA CL
> tau-t= 1.0 1.0 1.0 1.0
> ref-t= 335 335 335 335
>
>
>
> Thank you!
> --
> 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
>
> * For (un)subscribe requests visit
> 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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Re: [gmx-users] seeking help for generating combined trajectory files and clusters

[MD]

Hi Mark,

I looked the combined trajectory with VMD by loading the gro and xtc files,
and the ensemble looks messy (the ligand is flying away from the protein).
I am not sure which step could be causing the issue. But I want to describe
what I have done to the trajectory file from the beginning and hoping if
you could spot anything I did could be causing the issue?

After harvested the md.gro and md.xtc, I tried to correct the overflowing
issue with the following command:
gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -ur compact

Then I trimmed each trajectory file to ignore the first 10 ns.
gmx trjconv -f md_noPBC.xtc -s md.tpr -n md.ndx -pbc nojump -dt 50 -b 1
-e 20 -o md_round1_10-200ns.xtc

Then I combined the trajectory files together with the command I described
earlier (pasted below):
I did several 200 ns simulations and combined them into one trajectory file
with the commands:
gmx trjcat -f md_round1_10-200ns.xtc
 md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
-settime
I set the starting times to be: 10 ns, 190 ns, 380 ns

Then I made a RMSD matrix with the command:
gmx rms -f md_combined.xtc -f2 md_combined.xtc -s md.tpr -n md.ndx -m
 md_RMSD-matrix.xpm

Then I tried to build clusters with the command:
gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm md_RMSD-matrix.xpm
-method gromos -cl out.pdb -cutoff 0.2 -g out.log

Best,

MD

On Tue, Jan 22, 2019 at 10:19 AM Mark Abraham 
wrote:

> Hi,
>
> I can't tell, because I don't know what you did with the xtc files
> beforehand. But you should follow my earlier advice and visualize the
> combined trajectory and observe that this may be your problem before
> talking about it further. :-) Then see
>
> http://manual.gromacs.org/documentation/current/user-guide/terminology.html#suggested-workflow
>
> Mark
>
> On Tue, 22 Jan 2019 at 16:06 MD  wrote:
>
> > Hi Mark, yes that makes sense. Then how can I make trjconv avoid from
> > writing protein+ligand in different cells?
> > Ming
> >
> > On Tue, Jan 22, 2019 at 9:59 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > No, length has nothing to do with whether mdrun or trjconv may have
> > written
> > > different rounds in different representations (e.g. protein+ligand in
> the
> > > same periodic cell, or different cells).
> > >
> > > Mark
> > >
> > > On Tue, 22 Jan 2019 at 15:40 MD  wrote:
> > >
> > > > Thanks Mark.
> > > > When you said "mutually compatible periodic representation", did you
> > mean
> > > > they all have to have the same length of simulation? E.g. if one of
> > them
> > > > has a different length (91ns) and the rest all have 90 ns, the
> > combining
> > > > process will go wrong?
> > > >
> > > >
> > > > On Tue, Jan 22, 2019 at 4:13 AM Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You're comparing to the configurations in -f2, but that will only
> > make
> > > > > sense if the contents of the files for each round have mutually
> > > > compatible
> > > > > periodic representation. I suggest you visualise the combined
> > > trajectory
> > > > > and observe the problem.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, 21 Jan 2019 at 17:30 MD  wrote:
> > > > >
> > > > > > Hi Gromacs folks,
> > > > > >
> > > > > > I am trying to simulate protein and ligand compound.
> > > > > >
> > > > > > I did several 200 ns simulations and combined them into one
> > > trajectory
> > > > > file
> > > > > > with the commands:
> > > > > > gmx trjcat -f md_round1_10-200ns.xtc
> > > > > >  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc
> > -cat
> > > > > > -settime
> > > > > > I set the starting times to be: 10 ns, 190 ns, 380 ns
> > > > > >
> > > > > > Then I made a RMSD matrix with the command:
> > > > > > gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n
> > > md.ndx
> > > > -m
> > > > > > md_RMSD-matrix.xpm
> > > > > >
> > > > > > Then I tried to build clusters with the command:
> > > > > > gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm
> > > > > md_RMSD-matrix.xpm
> > > > > > -method gromos -cl out.pdb -cutoff 0.2 -g out.log
> > > > > >
> > > > > > There were 120 clusters came back. Except for the first and
> largest
> > > > > > cluster, all the rest of the clusters have a crazily far away
> > ligand
> > > > > > compared to where the protein is.
> > > > > >
> > > > > > I went back to look at each individual xtc from each round and
> > > produced
> > > > > > their own clusters and they all look good (no huge separation of
> > > > protein
> > > > > > and ligand).
> > > > > >
> > > > > > If all the xtc files are good on their own, how come the combined
> > xtc
> > > > is
> > > > > > giving me this result?
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > MD
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > >