Re: [gmx-users] Extracting trajectory

[Jorden Cabal]

Hi Anupama,

I understand your question. But I wonder why do you want all the explicit
water molecules within 5 Angstrom of your protein surface? That would be
meaningless until and unless you are intending to find the conserved water
molecules near the surface of protein. I don't understand your purpose, but
trjcat can not dynamically change the selection automatically at each frame
so directly it is not possible.

Instead you can get the trajectory in appropriate format by using the
"mindist" command which is used for calculating the contacts between two
groups.
Please see the options available with this command, you will find  "-ox"
option which will give you the required trajectory.

For example let's say,
original trajectory=traj.xtc
tpr=run.tpr
Index=index.ndx (group 1 for protein and 13 for sol)

the the command should look like this:
*gmx mindist -f traj.xtc -s run.tpr -n index.ndx -o output.out -n
output.xvg -ox required_traj.xtc -d 0.5 -group*

After being asked you will have to select appropriate group like 1 and 13
for protein and sol from the index file. The output file required_traj.xtc
will contain all the water molecules within 5 Angstrom of protein.
*Important Notes: *
   1: Since there are large number of water molecules in the system,
the calculation time will be very very high. I have not estimated so can
not comment on this  but I am sure that it will take a long.
   2: You will not be able to visualize the .xtc file directly using
visualization package like vmd as they require corresponding .gro file. But
in this case the index of the water molecules will change per frame so its
not possible. Instead you can directly write in the gro/pdb
formats.

*Although, I do not understand the purpose of your question, I still
suggest you to make intelligent choice of identifying water molecules near
to some interesting cavity instead of whole surface. This will save your
computational time. You can see the following paper for your reference.*

https://www.tandfonline.com/doi/abs/10.1080/1062936X.2018.1537301?journalCode=gsar20


I hope this will solve your problem.
Thank you

Jorden

On Wed, Oct 2, 2019 at 10:32 PM anupama sharma 
wrote:

> Dear users,
> I want to extract the trajectory of water molecules near the protein
> surface within 5 angstorm region. I was able to do that in using gmx select
> and gmx trjcat, but it is for only one time frame and than the water
> molecules diffuses away for the next time frame. I want to extract the
> trajectory of only those water molecules that are near protein surface
> within 5 angstorm region for each individual time frame so that i can get
> the complete trajectory of water molecules that are near the protein
> surface excluding the water molecules that diffuses away in each next
> frame..
> I will be thankful for help.
>
>
>
>
> Thanks and regards,
> Anupama
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[gmx-users] Extracting trajectory

[anupama sharma]

Dear users,
I want to extract the trajectory of water molecules near the protein
surface within 5 angstorm region. I was able to do that in using gmx select
and gmx trjcat, but it is for only one time frame and than the water
molecules diffuses away for the next time frame. I want to extract the
trajectory of only those water molecules that are near protein surface
within 5 angstorm region for each individual time frame so that i can get
the complete trajectory of water molecules that are near the protein
surface excluding the water molecules that diffuses away in each next
frame..
I will be thankful for help.




Thanks and regards,
Anupama
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Re: [gmx-users] extracting trajectory using trjconv

[Chenyu Liu]

Unfortunately, I have not seen similar situation before. The index could be
overlapping, for example: Protein, Non protein, water and chloride ions
where Non protein include the water and chloride ions. But I have not seen
the situation where the same name appears multiple times. I think you
should look into topology file to modify and solve the problem.
Good luck with that,
Chenyu

On Tue, Oct 1, 2019 at 7:24 PM Hadi Rahmaninejad 
wrote:

> Thank you Chenyu, but I thought there should be option for index file,
> however when I wanted to create an index file, for some reason my molecule
> appears two times and it gives me an error message of "having multiple same
> names" and cannot create the index file. Do you have any suggestions?
>
> Best,
> Hadi
>
> On Tue, Oct 1, 2019 at 5:14 PM Chenyu Liu  wrote:
>
> > I noticed that there are extra '*'s in my post, please ignore that (which
> > comes from the bold font I used
> > this should look good
> >
> > gmx_mpi energy -f npt.edr -o density.xvg < > Density
> > (Input2.)
> > EOF
> >
> >
> > On Tue, Oct 1, 2019 at 4:11 PM Chenyu Liu  wrote:
> >
> > > Hi Hadi,
> > >
> > > You can do this kind of option in this way (here is a part of my .pbs
> > file
> > > for submitting jobs):
> > >
> > >
> > > *gmx_mpi energy -f npt.edr -o density.xvg < > >
> > > *(Input2.)EOF*
> > >
> > > (Reference:
> > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> )
> > > The option is between the two 'EOF's. You need to run a few runs
> > > interactively to figure out what the inputs should be. Also, if you
> want
> > to
> > > do the same operation for multiple files, I would suggest checking out
> > bash
> > > programming for doing that.
> > > I hope this will help you.
> > >
> > > Chenyu Liu
> > >
> > > On Tue, Oct 1, 2019 at 3:46 PM Hadi Rahmaninejad <
> ha.rahma...@gmail.com>
> > > wrote:
> > >
> > >> Hello Gromacs Users,
> > >>
> > >> I am going to use "trjconv" to extract trajectory from a .trr file.
> Here
> > >> is
> > >> my command:
> > >> "gmx trjconv -f x.trr -s x.gro -o frames.gro"
> > >> then it gives me the options to choose my group, but I wanna it choose
> > for
> > >> me automatically, as I am going to extract from a lot of simulations
> > using
> > >> a loop. In another word, I need to give it the name of my projectile
> > >> molecule in the command line. Can anybody help me with this?
> > >>
> > >> Thank you in advance,
> > >> Hadi
> > >> --
> > >> 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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> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > >
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Re: [gmx-users] extracting trajectory using trjconv

[Hadi Rahmaninejad]

Thank you Chenyu, but I thought there should be option for index file,
however when I wanted to create an index file, for some reason my molecule
appears two times and it gives me an error message of "having multiple same
names" and cannot create the index file. Do you have any suggestions?

Best,
Hadi

On Tue, Oct 1, 2019 at 5:14 PM Chenyu Liu  wrote:

> I noticed that there are extra '*'s in my post, please ignore that (which
> comes from the bold font I used
> this should look good
>
> gmx_mpi energy -f npt.edr -o density.xvg < Density
> (Input2.)
> EOF
>
>
> On Tue, Oct 1, 2019 at 4:11 PM Chenyu Liu  wrote:
>
> > Hi Hadi,
> >
> > You can do this kind of option in this way (here is a part of my .pbs
> file
> > for submitting jobs):
> >
> >
> > *gmx_mpi energy -f npt.edr -o density.xvg < >
> > *(Input2.)EOF*
> >
> > (Reference:
> > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts)
> > The option is between the two 'EOF's. You need to run a few runs
> > interactively to figure out what the inputs should be. Also, if you want
> to
> > do the same operation for multiple files, I would suggest checking out
> bash
> > programming for doing that.
> > I hope this will help you.
> >
> > Chenyu Liu
> >
> > On Tue, Oct 1, 2019 at 3:46 PM Hadi Rahmaninejad 
> > wrote:
> >
> >> Hello Gromacs Users,
> >>
> >> I am going to use "trjconv" to extract trajectory from a .trr file. Here
> >> is
> >> my command:
> >> "gmx trjconv -f x.trr -s x.gro -o frames.gro"
> >> then it gives me the options to choose my group, but I wanna it choose
> for
> >> me automatically, as I am going to extract from a lot of simulations
> using
> >> a loop. In another word, I need to give it the name of my projectile
> >> molecule in the command line. Can anybody help me with this?
> >>
> >> Thank you in advance,
> >> Hadi
> >> --
> >> 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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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
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Re: [gmx-users] extracting trajectory using trjconv

[Chenyu Liu]

I noticed that there are extra '*'s in my post, please ignore that (which
comes from the bold font I used
this should look good

gmx_mpi energy -f npt.edr -o density.xvg < wrote:

> Hi Hadi,
>
> You can do this kind of option in this way (here is a part of my .pbs file
> for submitting jobs):
>
>
> *gmx_mpi energy -f npt.edr -o density.xvg <
> *(Input2.)EOF*
>
> (Reference:
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts)
> The option is between the two 'EOF's. You need to run a few runs
> interactively to figure out what the inputs should be. Also, if you want to
> do the same operation for multiple files, I would suggest checking out bash
> programming for doing that.
> I hope this will help you.
>
> Chenyu Liu
>
> On Tue, Oct 1, 2019 at 3:46 PM Hadi Rahmaninejad 
> wrote:
>
>> Hello Gromacs Users,
>>
>> I am going to use "trjconv" to extract trajectory from a .trr file. Here
>> is
>> my command:
>> "gmx trjconv -f x.trr -s x.gro -o frames.gro"
>> then it gives me the options to choose my group, but I wanna it choose for
>> me automatically, as I am going to extract from a lot of simulations using
>> a loop. In another word, I need to give it the name of my projectile
>> molecule in the command line. Can anybody help me with this?
>>
>> Thank you in advance,
>> Hadi
>> --
>> 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] extracting trajectory using trjconv

[Chenyu Liu]

Hi Hadi,

You can do this kind of option in this way (here is a part of my .pbs file
for submitting jobs):


*gmx_mpi energy -f npt.edr -o density.xvg  Hello Gromacs Users,
>
> I am going to use "trjconv" to extract trajectory from a .trr file. Here is
> my command:
> "gmx trjconv -f x.trr -s x.gro -o frames.gro"
> then it gives me the options to choose my group, but I wanna it choose for
> me automatically, as I am going to extract from a lot of simulations using
> a loop. In another word, I need to give it the name of my projectile
> molecule in the command line. Can anybody help me with this?
>
> Thank you in advance,
> Hadi
> --
> 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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[gmx-users] extracting trajectory using trjconv

[Hadi Rahmaninejad]

Hello Gromacs Users,

I am going to use "trjconv" to extract trajectory from a .trr file. Here is
my command:
"gmx trjconv -f x.trr -s x.gro -o frames.gro"
then it gives me the options to choose my group, but I wanna it choose for
me automatically, as I am going to extract from a lot of simulations using
a loop. In another word, I need to give it the name of my projectile
molecule in the command line. Can anybody help me with this?

Thank you in advance,
Hadi
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Re: [gmx-users] Extracting Trajectory and False Simulation

[João Henriques]

​The .top file is not useful for mdrun. It needs a .tpr that you create
using grompp, as you certainly had to do for the "ideal" simulation you
mention.

/J​

On Mon, Sep 7, 2015 at 8:36 AM, Rabindra Raj Oliya <oliyarabin...@gmail.com>
wrote:

> Thank you for your kind suggestions
> But how how can I use my alternative topology file in mdrun -rerun? I
> found no option to include topol.top in the synopsis you mentioned.
>
>
>
> Rabindra Raj Oliya
>
>  Original message 
> From: Tsjerk Wassenaar <tsje...@gmail.com>
> Date: 07/09/2015  11:57 AM  (GMT+05:45)
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>,Rabindra
> Raj Oliya <oliyarabin...@gmail.com>
> Subject: Re: [gmx-users] Extracting Trajectory and False Simulation
>
> Hi Rabindra,
>
> You can do an mdrun -rerun with the original trajectory and the
> alternative topology.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Sep 7, 2015 at 6:32 AM, Rabindra Raj Oliya <
> oliyarabin...@gmail.com> wrote:
> Actually I have two topology files corresponding to ideal and real system.
> Initially I have simulated using ideal topology.Now I have to false
> simulate using real topology as we have to ensemble average over the ideal
> configuration.
>
>
> Rabindra Raj Oliya
>
>  Original message 
> From: Justin Lemkul <jalem...@vt.edu>
> Date: 07/09/2015  7:43 AM  (GMT+05:45)
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Extracting Trajectory and False Simulation
>
>
>
> On 9/6/15 9:54 PM, Rabindra Oliya wrote:
> > Dear sir,
> > I have to extract the configuration stored into the trajectory file and
> > carry out the false simulation (in which we set up just one MD step and a
> > 0.0 time step) using the topology file. How can be this done?
> >
>
> Why bother?  A single step in which no time passes leaves you with the same
> coordinates you started with, which presumably you already have.
>
> If you want to extract coordinates from a trajectory into something you can
> visualize, use trjconv.
>
> -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] Extracting Trajectory and False Simulation

[Rabindra Raj Oliya]

Thank you for your kind suggestions
But how how can I use my alternative topology file in mdrun -rerun? I found no 
option to include topol.top in the synopsis you mentioned.



Rabindra Raj Oliya

 Original message 
From: Tsjerk Wassenaar <tsje...@gmail.com> 
Date: 07/09/2015  11:57 AM  (GMT+05:45) 
To: Discussion list for GROMACS users <gmx-us...@gromacs.org>,Rabindra Raj 
Oliya <oliyarabin...@gmail.com> 
Subject: Re: [gmx-users] Extracting Trajectory and False Simulation 
 
Hi Rabindra,

You can do an mdrun -rerun with the original trajectory and the alternative 
topology.

Cheers,

Tsjerk

On Mon, Sep 7, 2015 at 6:32 AM, Rabindra Raj Oliya <oliyarabin...@gmail.com> 
wrote:
Actually I have two topology files corresponding to ideal and real system.
Initially I have simulated using ideal topology.Now I have to false simulate 
using real topology as we have to ensemble average over the ideal configuration.


Rabindra Raj Oliya

 Original message 
From: Justin Lemkul <jalem...@vt.edu>
Date: 07/09/2015  7:43 AM  (GMT+05:45)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Extracting Trajectory and False Simulation



On 9/6/15 9:54 PM, Rabindra Oliya wrote:
> Dear sir,
> I have to extract the configuration stored into the trajectory file and
> carry out the false simulation (in which we set up just one MD step and a
> 0.0 time step) using the topology file. How can be this done?
>

Why bother?  A single step in which no time passes leaves you with the same
coordinates you started with, which presumably you already have.

If you want to extract coordinates from a trajectory into something you can
visualize, use trjconv.

-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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-- 
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Re: [gmx-users] Extracting Trajectory and False Simulation

[Tsjerk Wassenaar]

Hi Rabindra,

You can do an mdrun -rerun with the original trajectory and the alternative
topology.

Cheers,

Tsjerk

On Mon, Sep 7, 2015 at 6:32 AM, Rabindra Raj Oliya <oliyarabin...@gmail.com>
wrote:

> Actually I have two topology files corresponding to ideal and real system.
> Initially I have simulated using ideal topology.Now I have to false
> simulate using real topology as we have to ensemble average over the ideal
> configuration.
>
>
> Rabindra Raj Oliya
>
>  Original message 
> From: Justin Lemkul <jalem...@vt.edu>
> Date: 07/09/2015  7:43 AM  (GMT+05:45)
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Extracting Trajectory and False Simulation
>
>
>
> On 9/6/15 9:54 PM, Rabindra Oliya wrote:
> > Dear sir,
> > I have to extract the configuration stored into the trajectory file and
> > carry out the false simulation (in which we set up just one MD step and a
> > 0.0 time step) using the topology file. How can be this done?
> >
>
> Why bother?  A single step in which no time passes leaves you with the same
> coordinates you started with, which presumably you already have.
>
> If you want to extract coordinates from a trajectory into something you can
> visualize, use trjconv.
>
> -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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-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Extracting Trajectory and False Simulation

[Rabindra Raj Oliya]

Actually I have two topology files corresponding to ideal and real system.
Initially I have simulated using ideal topology.Now I have to false simulate 
using real topology as we have to ensemble average over the ideal configuration.


Rabindra Raj Oliya

 Original message 
From: Justin Lemkul <jalem...@vt.edu> 
Date: 07/09/2015  7:43 AM  (GMT+05:45) 
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] Extracting Trajectory and False Simulation 
 


On 9/6/15 9:54 PM, Rabindra Oliya wrote:
> Dear sir,
> I have to extract the configuration stored into the trajectory file and
> carry out the false simulation (in which we set up just one MD step and a
> 0.0 time step) using the topology file. How can be this done?
>

Why bother?  A single step in which no time passes leaves you with the same 
coordinates you started with, which presumably you already have.

If you want to extract coordinates from a trajectory into something you can 
visualize, use trjconv.

-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] Extracting Trajectory and False Simulation

[Justin Lemkul]

On 9/6/15 9:54 PM, Rabindra Oliya wrote:

Dear sir,
I have to extract the configuration stored into the trajectory file and
carry out the false simulation (in which we set up just one MD step and a
0.0 time step) using the topology file. How can be this done?



Why bother?  A single step in which no time passes leaves you with the same 
coordinates you started with, which presumably you already have.


If you want to extract coordinates from a trajectory into something you can 
visualize, use trjconv.


-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] Extracting Trajectory and False Simulation

[Rabindra Oliya]

Dear sir,
I have to extract the configuration stored into the trajectory file and
carry out the false simulation (in which we set up just one MD step and a
0.0 time step) using the topology file. How can be this done?
-- 
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