Re: [gmx-users] trajectory file

[Timofey Tyugashev]

16.12.2015 00:55, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
04.12.2015 14:43,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  
>?:

>>I ran the production MD and got the trajectory file (xtcformat) but as
>>I?m new to MD I don?t know how to visualize it. I opened it withvmd
>>and it could read the atoms and frames but didn?t show anything when
>>playingthe frames. I don?t know whether another program can do it or
>>my xtc is notcorrect.

>You can also read GROMACS trajectories with PyMOL. It offers quite
>nice visualisation options.
>Use 'load' command to load the coordinate file first, then load the
>trajectory itself using 'load_traj' command.

Only problem with pymol is that it eats very large amount of memory. I
cannot evel load trajectory of large nucleoprotein complex (~200k atoms
for complex itself without solvent) if it has ~1000 frames on
workstation with 64G ram.
Personally  I haven't noticed any qualitative difference in memory 
consumption compared with vmd when viewing same .xtc files. It either 
works or it does not. But my simulations are different (~5-10k atoms 
without solvent and tens of ns on 32G RAM system).
IIRC, there were some options in pymol for processing trajectories. 
Maybe they do influence the performance.

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Re: [gmx-users] trajectory file

[Alexey Shvetsov]

Timofey Tyugashev писал 15-12-2015 08:41:
04.12.2015 14:43, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
пишет:
I ran the production MD and got the trajectory file (xtcformat) but as 
I?m new to MD I don?t know how to visualize it. I opened it withvmd 
and it could read the atoms and frames but didn?t show anything when 
playingthe frames. I don?t know whether another program can do it or 
my xtc is notcorrect.

You can also read GROMACS trajectories with PyMOL. It offers quite
nice visualisation options.
Use 'load' command to load the coordinate file first, then load the
trajectory itself using 'load_traj' command.


Only problem with pymol is that it eats very large amount of memory. I 
cannot evel load trajectory of large nucleoprotein complex (~200k atoms 
for complex itself without solvent) if it has ~1000 frames on 
workstation with 64G ram.


--
Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexx...@gmail.com
mailto:ale...@omrb.pnpi.spb.ru
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Re: [gmx-users] trajectory file

[Timofey Tyugashev]

04.12.2015 14:43, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

I ran the production MD and got the trajectory file (xtcformat) but as I?m new 
to MD I don?t know how to visualize it. I opened it withvmd and it could read 
the atoms and frames but didn?t show anything when playingthe frames. I don?t 
know whether another program can do it or my xtc is notcorrect.
You can also read GROMACS trajectories with PyMOL. It offers quite nice 
visualisation options.
Use 'load' command to load the coordinate file first, then load the 
trajectory itself using 'load_traj' command.

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Re: [gmx-users] trajectory file

[mihammad roos]

Thank you all for your helpful answers. 


On Friday, December 4, 2015 4:35 PM, "Smith, Micholas D." 
<smit...@ornl.gov> wrote:
 

 Although you should ask these type of questions to the VMD mailing list, since 
the trjaectory file format is typical of md simulations from gromacs, I'll give 
you a quick answer:

VMD needs to know the atom names/types in order to draw anything, these are not 
stored in the xtc file. Instead you need to load your geometry into vmd first 
(your .gro or .pdb file) for your system, and then load the trajectory as data 
into the "molecule" that vmd generates on screen. Alternatively, you can use 
gmx trjconv to convert your trajectory file from xtc to pdb (or gro) and read 
the multi-frame pdb or gro file into vmd (these files will have multiple 
frames, and the atom names, but can be fairly large in terms of disk space).

Also, welcome to the wonderful world of MD simulations!

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Friday, December 04, 2015 7:29 AM
To: gmx-us...@gromacs.org; mihammad roos
Subject: Re: [gmx-users] trajectory file

On 12/3/15 4:39 PM, mihammad roos wrote:
> Hi everybody,
>
>
>
> I ran the production MD and got the trajectory file (xtcformat) but as I’m 
> new to MD I don’t know how to visualize it. I opened it withvmd and it could 
> read the atoms and frames but didn’t show anything when playingthe frames. I 
> don’t know whether another program can do it or my xtc is notcorrect.
>

Try some VMD tutorials. Loading coordinates and subsequently trajectories (as
data for those initial coordinates) is covered in any basic tutorial. Ask VMD
questions on the VMD mailing list.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] trajectory file

[Justin Lemkul]

On 12/3/15 4:39 PM, mihammad roos wrote:

Hi everybody,



I ran the production MD and got the trajectory file (xtcformat) but as I’m new 
to MD I don’t know how to visualize it. I opened it withvmd and it could read 
the atoms and frames but didn’t show anything when playingthe frames. I don’t 
know whether another program can do it or my xtc is notcorrect.



Try some VMD tutorials. Loading coordinates and subsequently trajectories (as 
data for those initial coordinates) is covered in any basic tutorial. Ask VMD 
questions on the VMD mailing list.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] trajectory file

[Smith, Micholas D.]

Although you should ask these type of questions to the VMD mailing list, since 
the trjaectory file format is typical of md simulations from gromacs, I'll give 
you a quick answer:

VMD needs to know the atom names/types in order to draw anything, these are not 
stored in the xtc file. Instead you need to load your geometry into vmd first 
(your .gro or .pdb file) for your system, and then load the trajectory as data 
into the "molecule" that vmd generates on screen. Alternatively, you can use 
gmx trjconv to convert your trajectory file from xtc to pdb (or gro) and read 
the multi-frame pdb or gro file into vmd (these files will have multiple 
frames, and the atom names, but can be fairly large in terms of disk space).

Also, welcome to the wonderful world of MD simulations!

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Friday, December 04, 2015 7:29 AM
To: gmx-us...@gromacs.org; mihammad roos
Subject: Re: [gmx-users] trajectory file

On 12/3/15 4:39 PM, mihammad roos wrote:
> Hi everybody,
>
>
>
> I ran the production MD and got the trajectory file (xtcformat) but as I’m 
> new to MD I don’t know how to visualize it. I opened it withvmd and it could 
> read the atoms and frames but didn’t show anything when playingthe frames. I 
> don’t know whether another program can do it or my xtc is notcorrect.
>

Try some VMD tutorials. Loading coordinates and subsequently trajectories (as
data for those initial coordinates) is covered in any basic tutorial. Ask VMD
questions on the VMD mailing list.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] trajectory file (xtc) visualization by VMD

[Homa rooz]

Hi guys!
I have  had a problem with VMD when reads frames on xtc file. It stops
suddenly. It seemed VMD is working out of memory so I remove solvent
molecules by trjconv command. It went further but still stops before the
end. What should I do? Can I remove some frame from the beginning part?
H​ow?​

-- 
Homa Ahmadi
Shahed University
Faculty of Basic Sciences
Alternative email> h.ahm...@shahed.ac.ir 
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