Re: [gmx-users] RMSD

[Justin Lemkul]

On 5/5/13 12:40 PM, Shima Arasteh wrote:

Hi,

I' like to know if it is possible to get the average RMSD through g_rms 
command? Or I need to get it manually?



Use g_analyze.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD from the average structure

[bipin singh]

Dear Sir,

Thanks for the useful insight.


On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund  wrote:

> Average coordinates are problematic and not generally representative.
> Consider for instance the average coordinates of a methyl group connected
> to X. The rotation around the C-X bond causes the average positions of the
> hydrogens to line up. Consider using g_cluster to find representative
> structures from your trajectory.
>
> Erik
>
> On 26 Apr 2013, at 06:59, bipin singh  wrote:
>
> > Thanks for your reply.
> > Actually I am interested to see how much structural deviation is
> occurring
> > in a protein during the simulation from its average position of atoms
> > rather than the initial position (crystal structure or starting
> structure).
> > The motivation of doing this analysis is the fact that in real solution
> > phase, a system may not be static and if we consider the time average
> > structure of a simulation to be the real representative of the structure
> in
> > solution phase rather than static crystal structure.
> >
> >
> >
> >
> >
> >
> >
> > On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar 
> wrote:
> >
> >> Hi Bipin Singh,
> >>
> >> That indeed gives you the RMSD against the average. Do think about it a
> bit
> >> more: do you want the average of the whole structure, or should you
> account
> >> for a phase of relaxation?
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >>
> >> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul  wrote:
> >>
> >>>
> >>>
> >>> On 4/24/13 3:06 AM, bipin singh wrote:
> >>>
>  Hi all,
> 
>  Please let me know whether this is the right way to calculate RMSD
> from
>  the
>  average structure from a simulation:
> 
>  g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
> 
> 
>  average.pdb: is the pdb file produced using -ox option of g_rmsf.
> 
> 
> >>> You can calculate RMSD with respect to whatever structure you like, but
> >>> the interpretation and justification for doing so are up to you.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==**==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>>
> >>> ==**==
> >>>
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >>> * Please search the archive at http://www.gromacs.org/**
> >>> Support/Mailing_Lists/Search<
> >> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> >> http://www.gromacs.org/Support/Mailing_Lists>
> >>>
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>
> >
> >
> >
> > --
> > *---
> > Thanks and Regards,
> > Bipin Singh*
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] RMSD from the average structure

[Erik Marklund]

Average coordinates are problematic and not generally representative. Consider 
for instance the average coordinates of a methyl group connected to X. The 
rotation around the C-X bond causes the average positions of the hydrogens to 
line up. Consider using g_cluster to find representative structures from your 
trajectory.

Erik

On 26 Apr 2013, at 06:59, bipin singh  wrote:

> Thanks for your reply.
> Actually I am interested to see how much structural deviation is occurring
> in a protein during the simulation from its average position of atoms
> rather than the initial position (crystal structure or starting structure).
> The motivation of doing this analysis is the fact that in real solution
> phase, a system may not be static and if we consider the time average
> structure of a simulation to be the real representative of the structure in
> solution phase rather than static crystal structure.
> 
> 
> 
> 
> 
> 
> 
> On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar  wrote:
> 
>> Hi Bipin Singh,
>> 
>> That indeed gives you the RMSD against the average. Do think about it a bit
>> more: do you want the average of the whole structure, or should you account
>> for a phase of relaxation?
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> 
>> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul  wrote:
>> 
>>> 
>>> 
>>> On 4/24/13 3:06 AM, bipin singh wrote:
>>> 
 Hi all,
 
 Please let me know whether this is the right way to calculate RMSD from
 the
 average structure from a simulation:
 
 g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
 
 
 average.pdb: is the pdb file produced using -ox option of g_rmsf.
 
 
>>> You can calculate RMSD with respect to whatever structure you like, but
>>> the interpretation and justification for doing so are up to you.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==**==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> 
>>> ==**==
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<
>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> http://www.gromacs.org/Support/Mailing_Lists>
>>> 
>> 
>> 
>> 
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> 
> 
> 
> -- 
> *---
> Thanks and Regards,
> Bipin Singh*
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Re: [gmx-users] RMSD from the average structure

[bipin singh]

Thanks for your reply.
Actually I am interested to see how much structural deviation is occurring
in a protein during the simulation from its average position of atoms
rather than the initial position (crystal structure or starting structure).
The motivation of doing this analysis is the fact that in real solution
phase, a system may not be static and if we consider the time average
structure of a simulation to be the real representative of the structure in
solution phase rather than static crystal structure.







On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar  wrote:

> Hi Bipin Singh,
>
> That indeed gives you the RMSD against the average. Do think about it a bit
> more: do you want the average of the whole structure, or should you account
> for a phase of relaxation?
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/24/13 3:06 AM, bipin singh wrote:
> >
> >> Hi all,
> >>
> >> Please let me know whether this is the right way to calculate RMSD from
> >> the
> >> average structure from a simulation:
> >>
> >> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
> >>
> >>
> >> average.pdb: is the pdb file produced using -ox option of g_rmsf.
> >>
> >>
> > You can calculate RMSD with respect to whatever structure you like, but
> > the interpretation and justification for doing so are up to you.
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> http://www.gromacs.org/Support/Mailing_Lists>
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
*---
Thanks and Regards,
Bipin Singh*
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Re: [gmx-users] RMSD from the average structure

[Tsjerk Wassenaar]

Hi Bipin Singh,

That indeed gives you the RMSD against the average. Do think about it a bit
more: do you want the average of the whole structure, or should you account
for a phase of relaxation?

Cheers,

Tsjerk


On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul  wrote:

>
>
> On 4/24/13 3:06 AM, bipin singh wrote:
>
>> Hi all,
>>
>> Please let me know whether this is the right way to calculate RMSD from
>> the
>> average structure from a simulation:
>>
>> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
>>
>>
>> average.pdb: is the pdb file produced using -ox option of g_rmsf.
>>
>>
> You can calculate RMSD with respect to whatever structure you like, but
> the interpretation and justification for doing so are up to you.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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-- 
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Re: [gmx-users] RMSD from the average structure

[Justin Lemkul]

On 4/24/13 3:06 AM, bipin singh wrote:

Hi all,

Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:

g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg


average.pdb: is the pdb file produced using -ox option of g_rmsf.



You can calculate RMSD with respect to whatever structure you like, but the 
interpretation and justification for doing so are up to you.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Erik Marklund]

On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote:




Thanks for your reply.
I want to chose one of the 5 conformers from a NMR PDB. As I studied  
in literature, the average structure could be selected regarding  
RMSD values and the go on with selected one to simulate in in water,  
lipid bilayer.
All right, I may make a matrix, but how would I chose my purposed  
conformers?



 Thanks for all your suggestions.

Sincerely,
Shima



From: Leandro Bortot 
To: Discussion list for GROMACS users 
Sent: Thursday, January 24, 2013 8:54 PM
Subject: Re: [gmx-users] RMSD

 you can make a simple script which calculates all the pairwise  
RMSD

values with g_rms. By doing this you can make a "RMSD matrix".


I think you can get the RMSD matrix from g_cluster in one go.



 The usefulness of this depends on what you are trying to see,  
which
wasn't clearly stated to us. I did it once because I wanted to know  
how

similar the 20 conformers from a NMR PDB actually were.



2013/1/24 FLOR MARTINI 

The values are OK, you obtain a value of RMSD of 0.2510229 . The  
value -1

refers time, and it is because you do not have a trajectory. You are
comparing only two .pdb structures, so it is consistent that you  
obtain

only one value, as you do not have more than one frame to compare.
Regards
Flor

Dra.M.Florencia Martini
Cátedra de Farmacotecnia II
Facultad de Farmacia y Bioquímica
Universidad de Buenos Aires
Junín 956 6º (1113)
TE: 54 011 4964-8273



  De: Shima Arasteh 
Para: Discussion list for GROMACS users 
Enviado: miércoles, 23 de enero de 2013 16:14
Asunto: Re: [gmx-users] RMSD

What I see in xvg file is as below:

# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@title "RMSD"
@xaxis  label "Time (ps)"
@yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "Protein after lsq fit to Protein"
   -1.0000.2510229


I though that -1 is the ref value and the other is the relative  
RMSD for
2.pdb. Is this -1 should be positive? What is this -1? Would you  
give me

any suggestions   please?


Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc:
Sent: Wednesday, January 23, 2013 9:36 PM
Subject: Re: [gmx-users] RMSD



On 1/23/13 12:48 PM, Shima Arasteh wrote:
I want to find the structure with the lowest RMSD, so I think it  
does

not make different to set any of pdb files as the ref structure.

I made an attempt and got the RMSD regarding the first pdb file. The
RMSD relative to -1 for the ref structure, is written in xvg file.  
Is my

approach logically correct?




The RMSD value should be positive, so I don't know how you get -1.   
Your
approach does not seem very sound - a structure does not have an  
absolute
RMSD value; it has an RMSD value relative to a reference structure,  
which

must be some sort of meaningful comparison or else you're not really
measuring anything useful.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Shima Arasteh]

Thanks for your reply.
I want to chose one of the 5 conformers from a NMR PDB. As I studied in 
literature, the average structure could be selected regarding RMSD values and 
the go on with selected one to simulate in in water, lipid bilayer.
All right, I may make a matrix, but how would I chose my purposed conformers?


 Thanks for all your suggestions.

Sincerely,
Shima



From: Leandro Bortot 
To: Discussion list for GROMACS users  
Sent: Thursday, January 24, 2013 8:54 PM
Subject: Re: [gmx-users] RMSD

     you can make a simple script which calculates all the pairwise RMSD
values with g_rms. By doing this you can make a "RMSD matrix".

     The usefulness of this depends on what you are trying to see, which
wasn't clearly stated to us. I did it once because I wanted to know how
similar the 20 conformers from a NMR PDB actually were.



2013/1/24 FLOR MARTINI 

> The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1
> refers time, and it is because you do not have a trajectory. You are
> comparing only two .pdb structures, so it is consistent that you obtain
> only one value, as you do not have more than one frame to compare.
> Regards
> Flor
>
> Dra.M.Florencia Martini
> Cátedra de Farmacotecnia II
> Facultad de Farmacia y Bioquímica
> Universidad de Buenos Aires
> Junín 956 6º (1113)
> TE: 54 011 4964-8273
>
>
> 
>  De: Shima Arasteh 
> Para: Discussion list for GROMACS users 
> Enviado: miércoles, 23 de enero de 2013 16:14
> Asunto: Re: [gmx-users] RMSD
>
> What I see in xvg file is as below:
>
> # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
> #
> # g_rms is part of G R O M A C S:
> #
> # Gromacs Runs On Most of All Computer Systems
> #
> @    title "RMSD"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "RMSD (nm)"
> @TYPE xy
> @ subtitle "Protein after lsq fit to Protein"
>   -1.000    0.2510229
>
>
> I though that -1 is the ref value and the other is the relative RMSD for
> 2.pdb. Is this -1 should be positive? What is this -1? Would you give me
> any suggestions   please?
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Discussion list for GROMACS users 
> Cc:
> Sent: Wednesday, January 23, 2013 9:36 PM
> Subject: Re: [gmx-users] RMSD
>
>
>
> On 1/23/13 12:48 PM, Shima Arasteh wrote:
> > I want to find the structure with the lowest RMSD, so I think it does
> not make different to set any of pdb files as the ref structure.
> > I made an attempt and got the RMSD regarding the first pdb file. The
> RMSD relative to -1 for the ref structure, is written in xvg file. Is my
> approach logically correct?
> >
>
> The RMSD value should be positive, so I don't know how you get -1.  Your
> approach does not seem very sound - a structure does not have an absolute
> RMSD value; it has an RMSD value relative to a reference structure, which
> must be some sort of meaningful comparison or else you're not really
> measuring anything useful.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] RMSD

[Leandro Bortot]

 you can make a simple script which calculates all the pairwise RMSD
values with g_rms. By doing this you can make a "RMSD matrix".

 The usefulness of this depends on what you are trying to see, which
wasn't clearly stated to us. I did it once because I wanted to know how
similar the 20 conformers from a NMR PDB actually were.



2013/1/24 FLOR MARTINI 

> The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1
> refers time, and it is because you do not have a trajectory. You are
> comparing only two .pdb structures, so it is consistent that you obtain
> only one value, as you do not have more than one frame to compare.
> Regards
> Flor
>
> Dra.M.Florencia Martini
> Cátedra de Farmacotecnia II
> Facultad de Farmacia y Bioquímica
> Universidad de Buenos Aires
> Junín 956 6º (1113)
> TE: 54 011 4964-8273
>
>
> 
>  De: Shima Arasteh 
> Para: Discussion list for GROMACS users 
> Enviado: miércoles, 23 de enero de 2013 16:14
> Asunto: Re: [gmx-users] RMSD
>
> What I see in xvg file is as below:
>
> # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
> #
> # g_rms is part of G R O M A C S:
> #
> # Gromacs Runs On Most of All Computer Systems
> #
> @title "RMSD"
> @xaxis  label "Time (ps)"
> @yaxis  label "RMSD (nm)"
> @TYPE xy
> @ subtitle "Protein after lsq fit to Protein"
>   -1.0000.2510229
>
>
> I though that -1 is the ref value and the other is the relative RMSD for
> 2.pdb. Is this -1 should be positive? What is this -1? Would you give me
> any suggestions   please?
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Discussion list for GROMACS users 
> Cc:
> Sent: Wednesday, January 23, 2013 9:36 PM
> Subject: Re: [gmx-users] RMSD
>
>
>
> On 1/23/13 12:48 PM, Shima Arasteh wrote:
> > I want to find the structure with the lowest RMSD, so I think it does
> not make different to set any of pdb files as the ref structure.
> > I made an attempt and got the RMSD regarding the first pdb file. The
> RMSD relative to -1 for the ref structure, is written in xvg file. Is my
> approach logically correct?
> >
>
> The RMSD value should be positive, so I don't know how you get -1.  Your
> approach does not seem very sound - a structure does not have an absolute
> RMSD value; it has an RMSD value relative to a reference structure, which
> must be some sort of meaningful comparison or else you're not really
> measuring anything useful.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> -- gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] RMSD

[FLOR MARTINI]

The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1 
refers time, and it is because you do not have a trajectory. You are comparing 
only two .pdb structures, so it is consistent that you obtain only one value, 
as you do not have more than one frame to compare.
Regards
Flor
 
Dra.M.Florencia Martini
Cátedra de Farmacotecnia II
Facultad de Farmacia y Bioquímica
Universidad de Buenos Aires
Junín 956 6º (1113)
TE: 54 011 4964-8273



 De: Shima Arasteh 
Para: Discussion list for GROMACS users  
Enviado: miércoles, 23 de enero de 2013 16:14
Asunto: Re: [gmx-users] RMSD
 
What I see in xvg file is as below:

# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg 
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@    title "RMSD"
@    xaxis  label "Time (ps)"
@    yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "Protein after lsq fit to Protein"
  -1.000    0.2510229


I though that -1 is the ref value and the other is the relative RMSD for 2.pdb. 
Is this -1 should be positive? What is this -1? Would you give me any 
suggestions   please?

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, January 23, 2013 9:36 PM
Subject: Re: [gmx-users] RMSD



On 1/23/13 12:48 PM, Shima Arasteh wrote:
> I want to find the structure with the lowest RMSD, so I think it does not 
> make different to set any of pdb files as the ref structure.
> I made an attempt and got the RMSD regarding the first pdb file. The RMSD 
> relative to -1 for the ref structure, is written in xvg file. Is my approach 
> logically correct?
> 

The RMSD value should be positive, so I don't know how you get -1.  Your 
approach does not seem very sound - a structure does not have an absolute RMSD 
value; it has an RMSD value relative to a reference structure, which must be 
some sort of meaningful comparison or else you're not really measuring anything 
useful.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Justin Lemkul]

On 1/23/13 1:14 PM, Shima Arasteh wrote:

What I see in xvg file is as below:

# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@title "RMSD"
@xaxis  label "Time (ps)"
@yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "Protein after lsq fit to Protein"
   -1.0000.2510229


I though that -1 is the ref value and the other is the relative RMSD for 2.pdb. 
Is this -1 should be positive? What is this -1? Would you give me any 
suggestions   please?



That is the value of time, normally read from a trajectory.  Please note that 
the "xaxis" label tells you this.  When no value is found (i.e. when comparing 
one structure to another, not part of a trajectory) there is no time value and 
thus g_rms prints -1.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Shima Arasteh]

What I see in xvg file is as below:

# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg 
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@    title "RMSD"
@    xaxis  label "Time (ps)"
@    yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "Protein after lsq fit to Protein"
  -1.000    0.2510229


I though that -1 is the ref value and the other is the relative RMSD for 2.pdb. 
Is this -1 should be positive? What is this -1? Would you give me any 
suggestions   please?

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, January 23, 2013 9:36 PM
Subject: Re: [gmx-users] RMSD



On 1/23/13 12:48 PM, Shima Arasteh wrote:
> I want to find the structure with the lowest RMSD, so I think it does not 
> make different to set any of pdb files as the ref structure.
> I made an attempt and got the RMSD regarding the first pdb file. The RMSD 
> relative to -1 for the ref structure, is written in xvg file. Is my approach 
> logically correct?
> 

The RMSD value should be positive, so I don't know how you get -1.  Your 
approach does not seem very sound - a structure does not have an absolute RMSD 
value; it has an RMSD value relative to a reference structure, which must be 
some sort of meaningful comparison or else you're not really measuring anything 
useful.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Justin Lemkul]

On 1/23/13 12:48 PM, Shima Arasteh wrote:

I want to find the structure with the lowest RMSD, so I think it does not make 
different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD 
relative to -1 for the ref structure, is written in xvg file. Is my approach 
logically correct?



The RMSD value should be positive, so I don't know how you get -1.  Your 
approach does not seem very sound - a structure does not have an absolute RMSD 
value; it has an RMSD value relative to a reference structure, which must be 
some sort of meaningful comparison or else you're not really measuring anything 
useful.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Shima Arasteh]

I want to find the structure with the lowest RMSD, so I think it does not make 
different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD 
relative to -1 for the ref structure, is written in xvg file. Is my approach 
logically correct?

Thanks for your suggestions.

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Wednesday, January 23, 2013 7:20 PM
Subject: Re: [gmx-users] RMSD



On 1/23/13 10:38 AM, Shima Arasteh wrote:
>
>
> Hi,
>
> Is it  possible to get RMSD of 10 different pdb files by GROMACS?

Relative to what?  Each other?  Some universal reference?

> g_rms may help?
>

That, or g_confrms, depending on what you're actually trying to measure.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] RMSD

[Da-Wei Li]

I think what you really need is not Gromacs.

For example, you can use UCSF Chimera to get alignment and RMSD between two
PDBs.


dawei


On Wed, Jan 23, 2013 at 10:38 AM, Shima Arasteh  wrote:

>
>
> Hi,
>
> Is it  possible to get RMSD of 10 different pdb files by GROMACS?
> g_rms may help?
>
>
> Sincerely,
> Shima
> --
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Re: [gmx-users] RMSD

[Justin Lemkul]

On 1/23/13 10:38 AM, Shima Arasteh wrote:



Hi,

Is it  possible to get RMSD of 10 different pdb files by GROMACS?


Relative to what?  Each other?  Some universal reference?


g_rms may help?



That, or g_confrms, depending on what you're actually trying to measure.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD plot

[Mark Abraham]

On 30/07/2012 4:49 PM, tarak karmakar wrote:

Dear Mark,

Thanks for the reply.

But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is continuing to increase and not getting equilibrium value. Is that
because my system is not minimized / equilibrated properly ?


Impossible to say... you have to look at the trajectory, and other 
observables.


Mark


Any suggestion ?

Thanks


On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham  wrote:

On 30/07/2012 3:39 AM, tarak karmakar wrote:

Dear All,

In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
trajectory with respect to the initial pdb structure. So as the pdb
had some short contacts, the resulting RMSD is showing large
increasing value around 0.4-0.5 nm.

1) Then, is it better to plot [ for reporting purpose ] the RMSD of
the trajectory with respect to the minimized coordinate file rather
than w. r. t. the initial PDB file?


Since neither of those configurations were sampled from the target ensemble,
it's a bit hard to say they make good reference states. Doing initial MD
with position restraints on the protein stops it moving much while the
ligand gets sorted out. Use that as the reference state from which you begin
production MD.

Better still, stop and consider how you will analyse your results before you
begin your simulation. Then you're better placed to do a simulation that
will lead to a meaningful result.



2) What is the acceptable range of RMSD for a protein simulation ? (
below 0.2 nm !! )


It depends on a whole host of things. There's no magic number.

Mark
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Re: [gmx-users] RMSD plot

[tarak karmakar]

Dear Mark,

Thanks for the reply.

But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is continuing to increase and not getting equilibrium value. Is that
because my system is not minimized / equilibrated properly ?
Any suggestion ?

Thanks


On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham  wrote:
> On 30/07/2012 3:39 AM, tarak karmakar wrote:
>>
>> Dear All,
>>
>> In my initial protein pdb structure I have added some external ligand
>> molecules and as a result of that there are several short contacts.
>> So, well, I minimized the system and then got the 'prot_min.gro' file.
>> Now after the equilibration run, I plotted the RMSD of the resulting
>> trajectory with respect to the initial pdb structure. So as the pdb
>> had some short contacts, the resulting RMSD is showing large
>> increasing value around 0.4-0.5 nm.
>>
>> 1) Then, is it better to plot [ for reporting purpose ] the RMSD of
>> the trajectory with respect to the minimized coordinate file rather
>> than w. r. t. the initial PDB file?
>
>
> Since neither of those configurations were sampled from the target ensemble,
> it's a bit hard to say they make good reference states. Doing initial MD
> with position restraints on the protein stops it moving much while the
> ligand gets sorted out. Use that as the reference state from which you begin
> production MD.
>
> Better still, stop and consider how you will analyse your results before you
> begin your simulation. Then you're better placed to do a simulation that
> will lead to a meaningful result.
>
>
>> 2) What is the acceptable range of RMSD for a protein simulation ? (
>> below 0.2 nm !! )
>
>
> It depends on a whole host of things. There's no magic number.
>
> Mark
> --
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Re: [gmx-users] RMSD plot

[Mark Abraham]

On 30/07/2012 3:39 AM, tarak karmakar wrote:

Dear All,

In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
trajectory with respect to the initial pdb structure. So as the pdb
had some short contacts, the resulting RMSD is showing large
increasing value around 0.4-0.5 nm.

1) Then, is it better to plot [ for reporting purpose ] the RMSD of
the trajectory with respect to the minimized coordinate file rather
than w. r. t. the initial PDB file?


Since neither of those configurations were sampled from the target 
ensemble, it's a bit hard to say they make good reference states. Doing 
initial MD with position restraints on the protein stops it moving much 
while the ligand gets sorted out. Use that as the reference state from 
which you begin production MD.


Better still, stop and consider how you will analyse your results before 
you begin your simulation. Then you're better placed to do a simulation 
that will lead to a meaningful result.



2) What is the acceptable range of RMSD for a protein simulation ? (
below 0.2 nm !! )


It depends on a whole host of things. There's no magic number.

Mark
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Re: [gmx-users] RMSD analysis during production MD

[Justin A. Lemkul]

Acoot Brett wrote:


 Dear All,
 
During a 1 ns production analysis (before it completes), I can analysis 
the RMSD by "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" 
without influence the normal calculation of the production analysis, right?
 


It's always safer to make a copy of the trajectory and do any sort of operation 
on it.  I doubt that mdrun and g_rms would conflict as far as creating errors in 
the calculations themselves, but you may run into simple I/O trouble if you've 
got multiple processes trying to open/close a trajectory file at the same time.


-Justin

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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] RMSD sudden jump

[Davide Mercadante]

Sorry I realized I attached the .xvg.

Here is a png for a easier visualization. Sorry for the inconvenience.

Thanks,
Davide

2012/3/14 Davide Mercadante 

> Hi Tsjerk,
>
> thanks very much for your prompt reply.
> I checked the last 5ns rmsd against an average structure calculated in the
> same time range and effectively the system seems to be converging (I
> attached the graph).
>
> However, the switch seems unlikely as the protein seems to lose part of
> its fold.?!
> Could that be an artifact of the forcefield or something similar?
>
> Should I repeat the MD using a different ff? Could this help?
>
> Thanks in advance for your reply.
>
> Cheers,
> Davide
>
>
> 2012/3/13 Tsjerk Wassenaar 
>
>> Hi Davide,
>>
>> If you've checked the trajectory, and you've assured that there are no
>> atoms wrapping over the periodic boundaries, and you've noticed a
>> sudden change in conformation, then probably that's what it is: a
>> sudden change in conformation. That does agree with the plot. After a
>> rather stationary phase, close to the reference structure, the
>> molecule undergoes a transition to another state. To see if it
>> converges in that state in the time of your simulations, get the
>> average structure from the last 5 ns of the simulation and run the
>> RMSD against that.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Tue, Mar 13, 2012 at 6:49 AM, Davide Mercadante
>>  wrote:
>> > Dear gromacs users,
>> >
>> > I have performed ~30ns MD on a protein in TIP4P water using the OPLS
>> > forcefield.
>> > I have concatenated the trajectories for each step using trjcat and
>> removed
>> > pbc effects using pbc nojump.
>> >
>> > All the particles of the system now don't jump anymore and the molecule
>> > doesn't appear as broken.
>> >
>> > However, at some point from the beginning of the simulation the RMSD
>> jumps
>> > up as in the graphs attached.
>> > Visualizing the trajectories from that point the protein just suddenly
>> > change conformation and its motions become faster (as testified by the
>> > RMSD).
>> >
>> > Can you please let me understand why this happens? If I have screwed
>> > something up with the calculation or if something due to the pbc
>> effects not
>> > removed properly?
>> > The same thing is also happening on a different simulations involving a
>> > mutant of this protein...
>> >
>> > Any help will be very much highly appreciated!
>> >
>> > Thank you!
>> > Davide
>> >
>> > --
>> > Davide Mercadante - PhD student -
>> > School of Chemical Sciences
>> > The University of Auckland
>> > 1142 Auckland, New Zealand
>> >
>> >
>> >
>> >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
> --
> Davide Mercadante - PhD student -
> School of Chemical Sciences
> The University of Auckland
> 1142 Auckland, New Zealand
>
>
>
>


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School of Chemical Sciences
The University of Auckland
1142 Auckland, New Zealand
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Re: [gmx-users] RMSD sudden jump

[Davide Mercadante]

Hi Tsjerk,

thanks very much for your prompt reply.
I checked the last 5ns rmsd against an average structure calculated in the
same time range and effectively the system seems to be converging (I
attached the graph).

However, the switch seems unlikely as the protein seems to lose part of its
fold.?!
Could that be an artifact of the forcefield or something similar?

Should I repeat the MD using a different ff? Could this help?

Thanks in advance for your reply.

Cheers,
Davide

2012/3/13 Tsjerk Wassenaar 

> Hi Davide,
>
> If you've checked the trajectory, and you've assured that there are no
> atoms wrapping over the periodic boundaries, and you've noticed a
> sudden change in conformation, then probably that's what it is: a
> sudden change in conformation. That does agree with the plot. After a
> rather stationary phase, close to the reference structure, the
> molecule undergoes a transition to another state. To see if it
> converges in that state in the time of your simulations, get the
> average structure from the last 5 ns of the simulation and run the
> RMSD against that.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Mar 13, 2012 at 6:49 AM, Davide Mercadante
>  wrote:
> > Dear gromacs users,
> >
> > I have performed ~30ns MD on a protein in TIP4P water using the OPLS
> > forcefield.
> > I have concatenated the trajectories for each step using trjcat and
> removed
> > pbc effects using pbc nojump.
> >
> > All the particles of the system now don't jump anymore and the molecule
> > doesn't appear as broken.
> >
> > However, at some point from the beginning of the simulation the RMSD
> jumps
> > up as in the graphs attached.
> > Visualizing the trajectories from that point the protein just suddenly
> > change conformation and its motions become faster (as testified by the
> > RMSD).
> >
> > Can you please let me understand why this happens? If I have screwed
> > something up with the calculation or if something due to the pbc effects
> not
> > removed properly?
> > The same thing is also happening on a different simulations involving a
> > mutant of this protein...
> >
> > Any help will be very much highly appreciated!
> >
> > Thank you!
> > Davide
> >
> > --
> > Davide Mercadante - PhD student -
> > School of Chemical Sciences
> > The University of Auckland
> > 1142 Auckland, New Zealand
> >
> >
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
Davide Mercadante - PhD student -
School of Chemical Sciences
The University of Auckland
1142 Auckland, New Zealand


rmsd_calpha_last5ns.xvg
Description: Binary data
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Re: [gmx-users] RMSD sudden jump

[Tsjerk Wassenaar]

Hi Davide,

If you've checked the trajectory, and you've assured that there are no
atoms wrapping over the periodic boundaries, and you've noticed a
sudden change in conformation, then probably that's what it is: a
sudden change in conformation. That does agree with the plot. After a
rather stationary phase, close to the reference structure, the
molecule undergoes a transition to another state. To see if it
converges in that state in the time of your simulations, get the
average structure from the last 5 ns of the simulation and run the
RMSD against that.

Cheers,

Tsjerk

On Tue, Mar 13, 2012 at 6:49 AM, Davide Mercadante
 wrote:
> Dear gromacs users,
>
> I have performed ~30ns MD on a protein in TIP4P water using the OPLS
> forcefield.
> I have concatenated the trajectories for each step using trjcat and removed
> pbc effects using pbc nojump.
>
> All the particles of the system now don't jump anymore and the molecule
> doesn't appear as broken.
>
> However, at some point from the beginning of the simulation the RMSD jumps
> up as in the graphs attached.
> Visualizing the trajectories from that point the protein just suddenly
> change conformation and its motions become faster (as testified by the
> RMSD).
>
> Can you please let me understand why this happens? If I have screwed
> something up with the calculation or if something due to the pbc effects not
> removed properly?
> The same thing is also happening on a different simulations involving a
> mutant of this protein...
>
> Any help will be very much highly appreciated!
>
> Thank you!
> Davide
>
> --
> Davide Mercadante - PhD student -
> School of Chemical Sciences
> The University of Auckland
> 1142 Auckland, New Zealand
>
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] RMSD value

[Mark Abraham]

On 9/01/2012 8:26 PM, madhumita das wrote:

Hi GROMACS Users,

  I have simulated a protein(pdb id 
3D9S) for 5 nanoseconds. This protein contains 978 residues and after 
5 nanoseconds I got 2.35 by comparing pdb structure with simulated 
one. I want to know is this value is ok or protein is disrupted?


Visualize your trajectory to get a handle on what this number means.

Mark
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Re: [gmx-users] RMSD

[shahid nayeem]

Thanks. But in timeline plugin of VMD I am able to measure RMSD with
respect to one of the frame of trajectory and I am interested to measure
RMSD with respect to another molecule. I am trying to measure RMSD of
trajectory frames with respect to Bound and unbound configuration of
molecule so that I can compare side chain configuration of trajectory with
bound and unbound sidechain configuration.  Please help.
Shahid Nayeem

On Tue, Nov 15, 2011 at 7:02 PM, felmer...@uchile.cl wrote:

> In any case, if you really want to see flexibility then you need RMSF and
> not RMSD as the later will only tell you about how similar is the
> configuration of a sidechain compared to a reference frame. If that is
> still what you want i think VMD has a tool for that in the timeline plugin.
>
>
>
> regards
>
>
>
> Felipe
>
> Mensaje original
> De: gianluca.sant...@ibs.fr
> Fecha: 15-nov-2011 10:18
> Para: "Discussion list for GROMACS users"
> Asunto: Re: [gmx-users] RMSD
>
>
> On 11/15/11 8:23 PM, shahid nayeem wrote:
>
> Dear all
> I am interested to get contour plot of residue RMSD vs time graph. I want
> to get the flexible and rigid regions of protein chain during simulation.
> g_rmsf does not gives me this plot.
> Please help
> shahid Nayeem
>
>
>
> Try g_rmsf -res , it could be useful, maybe.
>
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
> _
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
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Re: [gmx-users] RMSD

[felmer...@uchile.cl]

In any case, if you really want to see flexibility then you need RMSF and not 
RMSD as the later will only tell you about how similar is the configuration of 
a sidechain compared to a reference frame. If that is still what you want i 
think VMD has a tool for that in the timeline plugin.

 

regards

 

Felipe
Mensaje original De: gianluca.sant...@ibs.fr Fecha: 15-nov-2011 10:18 
Para: "Discussion list for GROMACS users" Asunto: Re: 
[gmx-users] RMSD   On 11/15/11 8:23 PM, shahid nayeem wrote:
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I 
want to get the flexible and rigid regions of protein chain during 
simulation. g_rmsf does not gives me this plot.
Please help
shahid Nayeem

  
Try g_rmsf -res , it could be useful, maybe. 
-- 
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html


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Re: [gmx-users] RMSD

[Gianluca Santoni]

On 11/15/11 8:23 PM, shahid nayeem wrote:

Dear all
I am interested to get contour plot of residue RMSD vs time graph. I 
want to get the flexible and rigid regions of protein chain during 
simulation. g_rmsf does not gives me this plot.

Please help
shahid Nayeem




Try g_rmsf -res , it could be useful, maybe.

--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

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Re: [gmx-users] RMSD bonds and angles

[Tsjerk Wassenaar]

Hey :)

If that is what you want, you'll have to turn to programming. But what do
you think to gain from it? First get to the bottom of things you can do with
gromacs already. Then, if the tools available don't help in answering your
question, think of what you'd need to get it done.

Cheers,

Tsjerk

On Oct 4, 2011 12:06 PM, "ahmet yıldırım"  wrote:


No, it calculates with respect to the positions atom. but I want to
calculate the RMSD bonds (A˚ ) and RMSD angles (o).

2011/10/4 Mark Abraham  > > On 4/10/2011 7:05 PM,
ahmet yıldırım wrote: >...

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Re: [gmx-users] RMSD bonds and angles

[ahmet yıldırım]

No, it calculates with respect to the positions atom. but I want to
calculate the RMSD bonds (A˚ ) and RMSD angles (o).

2011/10/4 Mark Abraham 

>  On 4/10/2011 7:05 PM, ahmet yıldırım wrote:
>
> any hints? :(
>
>
> You didn't find something useful in the section titled "Root mean square
> deviations in structure"?
>
> Mark
>
>
> 03 Ekim 2011 22:32 tarihinde ahmet yıldırım  yazdı:
>
>> I look at chapter 8 but I didnt found that I want. can you give a hint?
>> Thanks
>>
>>
>> 2011/10/3 Mark Abraham 
>>
>>> On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
>>>
 Dear users,

 How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?

>>>
>>>  Please start your search in chapter 8 of the manual, and consider doing
>>> some tutorial material. Someone is likely to have covered some similar
>>> procedures.
>>>
>>> Mark
>>>  --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
>>
>>
>>  --
>> Ahmet YILDIRIM
>>
>
>
>
> --
> Ahmet YILDIRIM
>
>
>
>
> --
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Re: [gmx-users] RMSD bonds and angles

[Mark Abraham]

On 4/10/2011 7:05 PM, ahmet y?ld?r?m wrote:

any hints? :(


You didn't find something useful in the section titled "Root mean square 
deviations in structure"?


Mark


03 Ekim 2011 22:32 tarihinde ahmet y?ld?r?m > yazd?:


I look at chapter 8 but I didnt found that I want. can you give a
hint?
Thanks


2011/10/3 Mark Abraham mailto:mark.abra...@anu.edu.au>>

On 3/10/2011 10:29 PM, ahmet y?ld?r?m wrote:

Dear users,

How can I calculate the RMSD bonds (A? ) and RMSD angles (o)?


Please start your search in chapter 8 of the manual, and
consider doing some tutorial material. Someone is likely to
have covered some similar procedures.

Mark
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Re: [gmx-users] RMSD bonds and angles

[ahmet yıldırım]

any hints? :(

03 Ekim 2011 22:32 tarihinde ahmet yıldırım  yazdı:

> I look at chapter 8 but I didnt found that I want. can you give a hint?
> Thanks
>
>
> 2011/10/3 Mark Abraham 
>
>> On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
>>
>>> Dear users,
>>>
>>> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?
>>>
>>
>> Please start your search in chapter 8 of the manual, and consider doing
>> some tutorial material. Someone is likely to have covered some similar
>> procedures.
>>
>> Mark
>> --
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>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>> Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet YILDIRIM
>



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Re: [gmx-users] RMSD bonds and angles

[ahmet yıldırım]

I look at chapter 8 but I didnt found that I want. can you give a hint?
Thanks

2011/10/3 Mark Abraham 

> On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
>
>> Dear users,
>>
>> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?
>>
>
> Please start your search in chapter 8 of the manual, and consider doing
> some tutorial material. Someone is likely to have covered some similar
> procedures.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] RMSD bonds and angles

[Mark Abraham]

On 3/10/2011 10:29 PM, ahmet yıldırım wrote:

Dear users,

How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?


Please start your search in chapter 8 of the manual, and consider doing 
some tutorial material. Someone is likely to have covered some similar 
procedures.


Mark
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Re: [gmx-users] RMSD with Vsite vs No Vsites

[Mark Abraham]

On 6/05/2011 5:32 PM, Sikandar Mashayak wrote:

well the deviations are about more than 0.5 nm..


And what does gmxcheck -s1 -s2 show?

Mark



On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai > wrote:


On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
> Hi
>
> As a test case, I did two simulations one the usual Protein in
Water and other with Vsites at COM of each monomer but these
Vsites dont interact with anyone else. I was expecting results of
these two should match almost exactly, but when I compare the rmsd
for Protein there seems to be discrepancy.
>
> I once again checked my Vsites definitions and set up, there
doesnt seem to be any error in definition as per my understanding.
>
> Is there any other reason that may be causing the mismatch? Or I
may have done something wrong in the setting up Vsites simulations.
>
> thanks
> sikandar

how large are the RMSD deviations? are they statistically
significant for
your needs? (i.e. if you only are about 1A scales, then RMSD
differences
< 0.05nm would be meaningless...

--
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu   | Birmingham AL
35294-4461
(205) 690-0808|
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Re: [gmx-users] RMSD with Vsite vs No Vsites

[Sikandar Mashayak]

well the deviations are about more than 0.5 nm..

On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai  wrote:

> On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
> > Hi
> >
> > As a test case, I did two simulations one the usual Protein in Water and
> other with Vsites at COM of each monomer but these Vsites dont interact with
> anyone else. I was expecting results of these two should match almost
> exactly, but when I compare the rmsd for Protein there seems to be
> discrepancy.
> >
> > I once again checked my Vsites definitions and set up, there doesnt seem
> to be any error in definition as per my understanding.
> >
> > Is there any other reason that may be causing the mismatch? Or I may have
> done something wrong in the setting up Vsites simulations.
> >
> > thanks
> > sikandar
>
> how large are the RMSD deviations? are they statistically significant for
> your needs? (i.e. if you only are about 1A scales, then RMSD differences
> < 0.05nm would be meaningless...
>
> --
> ===
> Peter C. Lai | University of Alabama-Birmingham
> Programmer/Analyst   | BEC 257
> Genetics, Div. of Research   | 1150 10th Avenue South
> p...@uab.edu  | Birmingham AL 35294-4461
> (205) 690-0808   |
> ===
>
>
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Re: [gmx-users] RMSD with Vsite vs No Vsites

[Peter C. Lai]

On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
> Hi
> 
> As a test case, I did two simulations one the usual Protein in Water and 
> other with Vsites at COM of each monomer but these Vsites dont interact with 
> anyone else. I was expecting results of these two should match almost 
> exactly, but when I compare the rmsd for Protein there seems to be 
> discrepancy.
> 
> I once again checked my Vsites definitions and set up, there doesnt seem to 
> be any error in definition as per my understanding.
> 
> Is there any other reason that may be causing the mismatch? Or I may have 
> done something wrong in the setting up Vsites simulations.
> 
> thanks
> sikandar

how large are the RMSD deviations? are they statistically significant for
your needs? (i.e. if you only are about 1A scales, then RMSD differences
< 0.05nm would be meaningless...

-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] RMSD with Vsite vs No Vsites

[Mark Abraham]

On 6/05/2011 2:21 AM, Sikandar Mashayak wrote:

Hi

As a test case, I did two simulations one the usual Protein in Water 
and other with Vsites at COM of each monomer but these Vsites dont 
interact with anyone else. I was expecting results of these two should 
match almost exactly, but when I compare the rmsd for Protein there 
seems to be discrepancy.


I once again checked my Vsites definitions and set up, there doesnt 
seem to be any error in definition as per my understanding.


Is there any other reason that may be causing the mismatch? Or I may 
have done something wrong in the setting up Vsites simulations.


GROMACS simulations are not intrinsically reproducible... 
http://www.gromacs.org/Documentation/Terminology/Reproducibility


Mark
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Re: [gmx-users] RMSD Calculation

[Tsjerk Wassenaar]

Hey :)

You probably want to fit on the protein and calculate the RMSD on the
ligand. You may need to specify these groups in an index file.

Hope it helps,

Tsjerk

On Mar 27, 2011 3:28 AM, "Justin A. Lemkul"  wrote:

Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small
molecule cocrystallized ligan...
I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html

If there's some reason you can't get that to work, then don't simply re-post
the same original question.  Iterative calls to g_rms are quite
straightforward to script.

-Justin

> Thank you very much, > Nancy >
-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD Calculation

[Justin A. Lemkul]

Nancy wrote:

Hi All,

I need to determine the RMSD of a small molecule cocrystallized ligand, 
against a large number of predicted docked conformations.  Please let me 
know what is the best method for doing this.




I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html

If there's some reason you can't get that to work, then don't simply re-post the 
same original question.  Iterative calls to g_rms are quite straightforward to 
script.


-Justin


Thank you very much,
Nancy



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD truncation Restart simulation problems

[Justin A. Lemkul]

Henri Mone wrote:

Hi Mark,

Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used "grompp" with the "-t state0.cpt"  option, are the starting
velocities taken from the cpt files or are the assigned randomly from
a Boltzman distribution.
Meaning are the new simulations starting fresh or are they
acontinuation from the previous ones?



The grompp output should tell you.  In older versions, when using a .trr file 
(with velocities) for a restart, the combination of -t traj.trr and "gen_vel = 
yes" caused the velocities in the .trr to be ignored and new ones generated.  A 
clear message was printed.


Check the screen output, and also compare the velocities in the .cpt with that 
of your new .tpr files using gmxcheck/gmxdump.


-Justin


Thanks,
Henri

On Tue, Mar 8, 2011 at 1:54 PM, Mark Abraham  wrote:

On 8/03/2011 9:41 PM, Henri Mone wrote:
Ah yes, I remember now. mdrun tries to be smart and
check that all the files match the state they were in before
the crash by computing checksums when writing and again
when reading.
So the original problem was that the steps recorded in the different
.cpt are different, unsurprisingly.
To fix this, get the .mdp used to make the original .tpr, and call
grompp the same way, plus (e.g.) -t state0.cpt for each of the
replicas. Now the (matching) state information will be taken by
grompp from the (matching) checkpoint files, and no checksum
calculation can fail. Then
mdrun_mpi -multi 32 -replex 5000 -s new.tpr
should be fine (and no .cpt should be provided).
While doing this, I would avoid trying to use mdrun -append,
by the way. Glue things together later if you need to.

Mark


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD truncation Restart simulation problems

[Henri Mone]

Hi Mark,

Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used "grompp" with the "-t state0.cpt"  option, are the starting
velocities taken from the cpt files or are the assigned randomly from
a Boltzman distribution.
Meaning are the new simulations starting fresh or are they
acontinuation from the previous ones?

Thanks,
Henri

On Tue, Mar 8, 2011 at 1:54 PM, Mark Abraham  wrote:
> On 8/03/2011 9:41 PM, Henri Mone wrote:
>Ah yes, I remember now. mdrun tries to be smart and
>check that all the files match the state they were in before
>the crash by computing checksums when writing and again
>when reading.
>So the original problem was that the steps recorded in the different
>.cpt are different, unsurprisingly.
>To fix this, get the .mdp used to make the original .tpr, and call
>grompp the same way, plus (e.g.) -t state0.cpt for each of the
>replicas. Now the (matching) state information will be taken by
>grompp from the (matching) checkpoint files, and no checksum
>calculation can fail. Then
>mdrun_mpi -multi 32 -replex 5000 -s new.tpr
>should be fine (and no .cpt should be provided).
>While doing this, I would avoid trying to use mdrun -append,
>by the way. Glue things together later if you need to.
>
>Mark
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Re: [gmx-users] RMSD truncation Restart simulation problems

[Mark Abraham]

On 8/03/2011 9:41 PM, Henri Mone wrote:

Hi All, hi Mark,
Here are some more details. The outputs and error messages are
attached at the end of the e-mail. After truncation I get the error
message [1a], gromacs has problems with the checksum of the trr fles.
After truncation the trajectories (xtc, trr) have the same length of
27752 frames [1b]. All the edr files have the same length of 277518
frames [1b]. The cpt files used after truncation have a step =
138762700 and t = 277525.40 [1c].
Before truncation I got the error message [2], gromacs complains that
the 32 subsystems are not compatible.
Anyone a idea was is going wrong?

Thanks,
Henri



1a: AFTER TRUNCATION: ERROR MESSAGE
Reading checkpoint file state1.cpt generated: Thu Jan 27 02:19:50 2011
   #PME-nodes mismatch,
 current program: -1
 checkpoint file: 0
Reading checkpoint file state2.cpt generated: Thu Jan 27 02:19:50 2011
   #PME-nodes mismatch,
 current program: -1
 checkpoint file: 0
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.
...
---
Program mdrun_mpi, VERSION 4.5.3
Source code file: checkpoint.c, line: 1767
Fatal error:
Can't read 1048576 bytes of 'traj1.trr' to compute checksum. The file
has been replaced or its contents has been modified.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
---
Program mdrun_mpi, VERSION 4.5.3
Source code file: checkpoint.c, line: 1767
Fatal error:
Can't read 1048576 bytes of 'traj2.trr' to compute checksum. The file
has been replaced or its contents has been modified.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 32
gcq#307: "Good Music Saves your Soul" (Lemmy)
[n030212:18418] MPI_ABORT invoked on rank 1 in communicator
MPI_COMM_WORLD with errorcode -1


Ah yes, I remember now. mdrun tries to be smart and check that all the 
files match the state they were in before the crash by computing 
checksums when writing and again when reading.





1b: AFTER TRUNCATION: XTC TRR
$ gmxcheck -f traj0.xtc
Checking file traj0.xtc
Reading frame   0 time0.000
# Atoms  224
Precision 0.001 (nm)
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   0
Coords   2775210
Velocities   0
Forces   0
Box  2775210
...
$ gmxcheck -f traj31.xtc
Checking file traj31.xtc
Reading frame   0 time0.000
# Atoms  224
Precision 0.001 (nm)
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   0
Coords   2775210
Velocities   0
Forces   0
Box  2775210

$ gmxcheck -f traj0.trr
Checking file traj0.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  6647
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   2775210
Coords   2775210
Velocities   2775210
Forces   0
Box  2775210
$ gmxcheck -f traj1.trr
Checking file traj1.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  6647
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   2775210
Coords   2775210
Velocities   2775210
Forces   0
Box  2775210
...
$ gmxcheck -f traj31.trr
Checking file traj31.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  6647
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   2775210
Coords   2775210
Velocities   2775210
Forces   0
Box  2775210

$ eneconv -f ener0.edr
Reading energy frame  0 time0.000
Continue writing frames from t=0, step=0
Last energy frame read 138759 time 277518.000 iting frame time
276000
Last step written from ener0.edr: t 277518, step 138759000
Last frame written was at step 138759000, time 277518.00
Wrote 138760 frames
...
$ eneconv -f ener31.edr
Reading energy frame  0 time0.000
Continue writing frames from t=0, step=0
Last energy frame read 138759 time 277518.000 iting frame time
276000
Last step written from ener31.edr: t 277518, step 138759000
Last frame written was at step 138759000, time 277518.00
Wr

Re: [gmx-users] RMSD truncation Restart simulation problems

[Henri Mone]

Hi All, hi Mark,
Here are some more details. The outputs and error messages are
attached at the end of the e-mail. After truncation I get the error
message [1a], gromacs has problems with the checksum of the trr fles.
After truncation the trajectories (xtc, trr) have the same length of
27752 frames [1b]. All the edr files have the same length of 277518
frames [1b]. The cpt files used after truncation have a step =
138762700 and t = 277525.40 [1c].
Before truncation I got the error message [2], gromacs complains that
the 32 subsystems are not compatible.
Anyone a idea was is going wrong?

Thanks,
Henri



1a: AFTER TRUNCATION: ERROR MESSAGE
Reading checkpoint file state1.cpt generated: Thu Jan 27 02:19:50 2011
  #PME-nodes mismatch,
current program: -1
checkpoint file: 0
Reading checkpoint file state2.cpt generated: Thu Jan 27 02:19:50 2011
  #PME-nodes mismatch,
current program: -1
checkpoint file: 0
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.
...
---
Program mdrun_mpi, VERSION 4.5.3
Source code file: checkpoint.c, line: 1767
Fatal error:
Can't read 1048576 bytes of 'traj1.trr' to compute checksum. The file
has been replaced or its contents has been modified.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
---
Program mdrun_mpi, VERSION 4.5.3
Source code file: checkpoint.c, line: 1767
Fatal error:
Can't read 1048576 bytes of 'traj2.trr' to compute checksum. The file
has been replaced or its contents has been modified.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 32
gcq#307: "Good Music Saves your Soul" (Lemmy)
[n030212:18418] MPI_ABORT invoked on rank 1 in communicator
MPI_COMM_WORLD with errorcode -1



1b: AFTER TRUNCATION: XTC TRR
$ gmxcheck -f traj0.xtc
Checking file traj0.xtc
Reading frame   0 time0.000
# Atoms  224
Precision 0.001 (nm)
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   0
Coords   2775210
Velocities   0
Forces   0
Box  2775210
...
$ gmxcheck -f traj31.xtc
Checking file traj31.xtc
Reading frame   0 time0.000
# Atoms  224
Precision 0.001 (nm)
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   0
Coords   2775210
Velocities   0
Forces   0
Box  2775210

$ gmxcheck -f traj0.trr
Checking file traj0.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  6647
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   2775210
Coords   2775210
Velocities   2775210
Forces   0
Box  2775210
$ gmxcheck -f traj1.trr
Checking file traj1.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  6647
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   2775210
Coords   2775210
Velocities   2775210
Forces   0
Box  2775210
...
$ gmxcheck -f traj31.trr
Checking file traj31.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  6647
Reading frame   27000 time 27.000
Item#frames Timestep (ps)
Step 2775210
Time 2775210
Lambda   2775210
Coords   2775210
Velocities   2775210
Forces   0
Box  2775210

$ eneconv -f ener0.edr
Reading energy frame  0 time0.000
Continue writing frames from t=0, step=0
Last energy frame read 138759 time 277518.000 iting frame time
276000
Last step written from ener0.edr: t 277518, step 138759000
Last frame written was at step 138759000, time 277518.00
Wrote 138760 frames
...
$ eneconv -f ener31.edr
Reading energy frame  0 time0.000
Continue writing frames from t=0, step=0
Last energy frame read 138759 time 277518.000 iting frame time
276000
Last step written from ener31.edr: t 277518, step 138759000
Last frame written was at step 138759000, time 277518.00
Wrote 138760 frames





1c: AFTER TRUNCATION: CPT
state0.cpt:
generation time = Thu Jan 27 02:19:50 2011
step = 138762700
t = 277525.40
...
state31.cpt:
generation time = Thu Jan 27 02:19:50 2011
step = 138762700
t = 277525.40

Re: [gmx-users] RMSD truncation Restart simulation problems

[Mark Abraham]

On 7/03/2011 8:23 PM, Henri Mone wrote:

Dear Gromacs Users/ Experts and Beginners,

I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations
stooped abruptly and therefore the replicas have uneven information.
One of the checkpoint differ in time and frame compared to other
replicas.  My case is very similar to the problem reported in the
Gromacs mailinglist [1].
I did what was suggest in the above [1] to truncate all the
trajectories to a previous checkpoint which is available (I have
extensive checkpoint files backups). Even after truncation it does not
work. Gromacs terminates immediately after realizing the files got
truncated.


What does gmxcheck say about the time step in each of your .cpt files? 
Before and after you played with things?


What messages accompany the termination? We can't help you without 
diagnostic data :-)


Mark
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Re: [gmx-users] RMSD and Resolution

[Tsjerk Wassenaar]

Hi Ahmet,

I'm not sure whether it's been checked. It has been found that NMR
structures tend to yield larger deviations than crystal structures. If
you're going to try, due make sure to compensate for other potential
influences, such as the size and sphericity of the proteins.

Cheers,

Tsjerk

2010/11/25 ahmet yıldırım :
> Hi,
>
> Is there a relationship between RMSD value obtained from the calculation and
> Resolution value in PDB file?
>
> Thanks in advance
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] rmsd between different monomers

[Mark Abraham]

On 9/05/2010 10:01 PM, Anupam Nath Jha wrote:


Ok.

But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out

it ask me groups... and that i thought is for fitting///

for example -


Select group for least squares fit
Group 0 (C-alpha_chain1) has   249 elements
Group 1 (C-alpha_chain2) has   249 elements
Group 2 (C-alpha_chain3) has   249 elements
Group 3 (C-alpha_chain4) has   249 elements
Select a group: 0
Selected 0: 'C-alpha_chain1'


So group 0 in *each* structure is used for fitting the two structures to 
each other...



Select group for RMSD calculation
Group 0 (C-alpha_chain1) has   249 elements
Group 1 (C-alpha_chain2) has   249 elements
Group 2 (C-alpha_chain3) has   249 elements
Group 3 (C-alpha_chain4) has   249 elements
Select a group:1
Selected 1: 'C-alpha_chain2'


... and group 1 in *each* structure is then used for the RMSD calculation.

The above is *not* fitting group 0 to group 1, and then measuring the 
RMSD of group 0 w.r.t. group 1, which sounds about what you want to do. 
You need my editconf/trjconv approach for that.


It's up to you to determine whether groups 0 and 1 should intersect. 
This allows you to (say) do an all-C-alpha fit, and then measure only 
the part of interest. In your case, as Justin said, since the two input 
structures are the same, you get zero RMSD regardless what else you do.


Notice how giving the command line, inputs and outputs has led to 
getting useful feedback, rather than the last 10 emails' worth of 
frustration because nobody knows what the other is talking about :-)


Mark
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Re: [gmx-users] rmsd between different monomers

[Bharath.K. Chakravarthi]

you said you have used online server for superimposition ...
which one you used...
try TOPMATCH server

On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha wrote:

>
> Ok.
>
> But when I run this command
> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>
> it ask me groups... and that i thought is for fitting///
>
> for example -
>
> 
> Select group for least squares fit
> Group 0 (C-alpha_chain1) has   249 elements
> Group 1 (C-alpha_chain2) has   249 elements
> Group 2 (C-alpha_chain3) has   249 elements
> Group 3 (C-alpha_chain4) has   249 elements
> Select a group: 0
> Selected 0: 'C-alpha_chain1'
> Select group for RMSD calculation
> Group 0 (C-alpha_chain1) has   249 elements
> Group 1 (C-alpha_chain2) has   249 elements
> Group 2 (C-alpha_chain3) has   249 elements
> Group 3 (C-alpha_chain4) has   249 elements
> Select a group:1
> Selected 1: 'C-alpha_chain2'
>
> -
>
> Is it not superimposing these two chins and calculating RMSD between
> them???
>
> --
> anupam
>
>
> > On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:
> >>
> >>
> >> Anupam Nath Jha wrote:
> 
>  Anupam Nath Jha wrote:
> > Dear all
> >
> > I made an index file with 4 different groups for 4 different chains
> > (since my
> > protein is a tetramer) and then run
> >
> > g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
> >
> > to get the rmsd between two different monomers from the same
> structure,
> > it asked me two different groups and I gave 0 and 1.
> >
> > The output file is like this
> >
> > # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
> > #
> > # g_rms is part of G R O M A C S:
> > #
> > # Grunge ROck MAChoS
> > #
> > @ title "RMSD"
> > @ xaxis label "Time (ps)"
> > @ yaxis label "RMSD (nm)"
> > @TYPE xy
> > @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
> > 0.000 0.001
> >
>  In the command you've given (with the same file for -s and -f),
>  you're computing
>  the RMSD at time zero, after fitting to the structure at time zero,
>  so the RMSD
>  must be zero.
> >>>
> >>>
> >>> but I am giving different groups (as chains). I am trying to get RMSD
> >>> between
> >>> two monomers in same structure so what's wrong in that
> >>>
> >>
> >> It doesn't matter. The structure for calculation (-f) and the reference
> >> structure (-s) are identical, so the RMSD has to be zero, regardless of
> >> the fitting group and calculation groups chosen.
> >
> > Exactly. Only if you can fit group A from one file to group B from a
> > file (which may or may not be the same file) can Anupam do this
> > calculation. g_rms seems not to allow this.
> >
> > Instead, Anupam should use trjconv or editconf to select groups
> > beforehand, as I think I suggested a few days back. Thus (say) editconf
> > produces file_with_group_A.pdb and editconf produces
> > file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s
> > file_with_group_B. This will work if the two groups have the same atoms
> > in matching orders, which should be the case for a tetramer setup.
> >
> > Mark
> >
> > so the rmsd = 0.001
> >
> > whereas when I use online server it gives me 1.4.
> >
> > so what am I doing wrong?
> >
>  Then whatever you're giving the online server is different. The
> Gromacs
>  calculation seems to be correct.
> 
>  -Justin
> 
> >>>
> >>>
> >>>
> > regrads
> > anupam
> >
> >
> >
>  --
>  
> 
>  Justin A. Lemkul
>  Ph.D. Candidate
>  ICTAS Doctoral Scholar
>  MILES-IGERT Trainee
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>  
>  --
>  gmx-users mailing list gmx-users@gromacs.org
>  http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before
>  posting!
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> 
>  --
>  This message has been scanned for viruses and
>  dangerous content by MailScanner, and is
>  believed to be clean.
> 
> 
> >>>
> >>>
> >>
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
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> > Can't post? Read http://www.gromacs.org/mail

Re: [gmx-users] rmsd between different monomers

[Anupam Nath Jha]

Ok.

But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out

it ask me groups... and that i thought is for fitting///

for example -


Select group for least squares fit
Group 0 (C-alpha_chain1) has   249 elements
Group 1 (C-alpha_chain2) has   249 elements
Group 2 (C-alpha_chain3) has   249 elements
Group 3 (C-alpha_chain4) has   249 elements
Select a group: 0
Selected 0: 'C-alpha_chain1'
Select group for RMSD calculation
Group 0 (C-alpha_chain1) has   249 elements
Group 1 (C-alpha_chain2) has   249 elements
Group 2 (C-alpha_chain3) has   249 elements
Group 3 (C-alpha_chain4) has   249 elements
Select a group:1
Selected 1: 'C-alpha_chain2'

-

Is it not superimposing these two chins and calculating RMSD between them???

--
anupam


> On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:
>>
>>
>> Anupam Nath Jha wrote:

 Anupam Nath Jha wrote:
> Dear all
>
> I made an index file with 4 different groups for 4 different chains
> (since my
> protein is a tetramer) and then run
>
> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>
> to get the rmsd between two different monomers from the same structure,
> it asked me two different groups and I gave 0 and 1.
>
> The output file is like this
>
> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
> #
> # g_rms is part of G R O M A C S:
> #
> # Grunge ROck MAChoS
> #
> @ title "RMSD"
> @ xaxis label "Time (ps)"
> @ yaxis label "RMSD (nm)"
> @TYPE xy
> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
> 0.000 0.001
>
 In the command you've given (with the same file for -s and -f),
 you're computing
 the RMSD at time zero, after fitting to the structure at time zero,
 so the RMSD
 must be zero.
>>>
>>>
>>> but I am giving different groups (as chains). I am trying to get RMSD
>>> between
>>> two monomers in same structure so what's wrong in that
>>>
>>
>> It doesn't matter. The structure for calculation (-f) and the reference
>> structure (-s) are identical, so the RMSD has to be zero, regardless of
>> the fitting group and calculation groups chosen.
>
> Exactly. Only if you can fit group A from one file to group B from a
> file (which may or may not be the same file) can Anupam do this
> calculation. g_rms seems not to allow this.
>
> Instead, Anupam should use trjconv or editconf to select groups
> beforehand, as I think I suggested a few days back. Thus (say) editconf
> produces file_with_group_A.pdb and editconf produces
> file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s
> file_with_group_B. This will work if the two groups have the same atoms
> in matching orders, which should be the case for a tetramer setup.
>
> Mark
>
> so the rmsd = 0.001
>
> whereas when I use online server it gives me 1.4.
>
> so what am I doing wrong?
>
 Then whatever you're giving the online server is different. The Gromacs
 calculation seems to be correct.

 -Justin

>>>
>>>
>>>
> regrads
> anupam
>
>
>
 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing list gmx-users@gromacs.org
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 posting!
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 believed to be clean.


>>>
>>>
>>
> --
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>
>


-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



--

Re: [gmx-users] rmsd between different monomers

[Mark Abraham]

On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:



Anupam Nath Jha wrote:


Anupam Nath Jha wrote:

Dear all

I made an index file with 4 different groups for 4 different chains
(since my
protein is a tetramer) and then run

g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out

to get the rmsd between two different monomers from the same structure,
it asked me two different groups and I gave 0 and 1.

The output file is like this

# g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
#
# g_rms is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "RMSD"
@ xaxis label "Time (ps)"
@ yaxis label "RMSD (nm)"
@TYPE xy
@ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
0.000 0.001


In the command you've given (with the same file for -s and -f),
you're computing
the RMSD at time zero, after fitting to the structure at time zero,
so the RMSD
must be zero.



but I am giving different groups (as chains). I am trying to get RMSD
between
two monomers in same structure so what's wrong in that



It doesn't matter. The structure for calculation (-f) and the reference
structure (-s) are identical, so the RMSD has to be zero, regardless of
the fitting group and calculation groups chosen.


Exactly. Only if you can fit group A from one file to group B from a 
file (which may or may not be the same file) can Anupam do this 
calculation. g_rms seems not to allow this.


Instead, Anupam should use trjconv or editconf to select groups 
beforehand, as I think I suggested a few days back. Thus (say) editconf 
produces file_with_group_A.pdb and editconf produces 
file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s 
file_with_group_B. This will work if the two groups have the same atoms 
in matching orders, which should be the case for a tetramer setup.


Mark


so the rmsd = 0.001

whereas when I use online server it gives me 1.4.

so what am I doing wrong?


Then whatever you're giving the online server is different. The Gromacs
calculation seems to be correct.

-Justin






regrads
anupam




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] rmsd between different monomers

[Justin A. Lemkul]

Anupam Nath Jha wrote:


Anupam Nath Jha wrote:

Dear all

I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run

g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out

to get the rmsd between two different monomers from the same structure,
it asked me two different groups and I gave 0 and 1.

The output file is like this

# g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
#
# g_rms is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@title "RMSD"
@xaxis  label "Time (ps)"
@yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
   0.0000.001


In the command you've given (with the same file for -s and -f), you're computing
the RMSD at time zero, after fitting to the structure at time zero, so the RMSD
must be zero.



but I am giving different groups (as chains). I am trying to get RMSD between
two monomers in same structure so what's wrong in that



It doesn't matter.  The structure for calculation (-f) and the reference 
structure (-s) are identical, so the RMSD has to be zero, regardless of the 
fitting group and calculation groups chosen.


-Justin


-
anupam


so the rmsd = 0.001

whereas when I use online server it gives me 1.4.

so what am I doing wrong?


Then whatever you're giving the online server is different.  The Gromacs
calculation seems to be correct.

-Justin






regrads
anupam




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] rmsd between different monomers

[Anupam Nath Jha]

>
>
> Anupam Nath Jha wrote:
>> Dear all
>>
>> I made an index file with 4 different groups for 4 different chains (since my
>> protein is a tetramer) and then run
>>
>> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>>
>> to get the rmsd between two different monomers from the same structure,
>> it asked me two different groups and I gave 0 and 1.
>>
>> The output file is like this
>>
>> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
>> #
>> # g_rms is part of G R O M A C S:
>> #
>> # Grunge ROck MAChoS
>> #
>> @title "RMSD"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "RMSD (nm)"
>> @TYPE xy
>> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
>>0.0000.001
>>
>
> In the command you've given (with the same file for -s and -f), you're 
> computing
> the RMSD at time zero, after fitting to the structure at time zero, so the 
> RMSD
> must be zero.


but I am giving different groups (as chains). I am trying to get RMSD between
two monomers in same structure so what's wrong in that

-
anupam

>>
>> so the rmsd = 0.001
>>
>> whereas when I use online server it gives me 1.4.
>>
>> so what am I doing wrong?
>>
>
> Then whatever you're giving the online server is different.  The Gromacs
> calculation seems to be correct.
>
> -Justin
>



>> regrads
>> anupam
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



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Re: [gmx-users] rmsd between different monomers

[Justin A. Lemkul]

Itamar Kass wrote:

Hi Anupam ,

To me it seems that you have used the the wrong groups for the RMSD, you
actually compare the protein to himself. Have a second look on at the
group contact, you groups should be numbered 12 or higher.



Not in this case.  The headers of the .xvg file in the original post indicate 
that the correct custom groups were used.  If one deletes the default groups, 
then the numbering will be completely different.


-Justin



cheers,
Itamar




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] rmsd between different monomers

[Justin A. Lemkul]

Anupam Nath Jha wrote:

Dear all

I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run

g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out

to get the rmsd between two different monomers from the same structure,
it asked me two different groups and I gave 0 and 1.

The output file is like this

# g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
#
# g_rms is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@title "RMSD"
@xaxis  label "Time (ps)"
@yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
   0.0000.001



In the command you've given (with the same file for -s and -f), you're computing 
the RMSD at time zero, after fitting to the structure at time zero, so the RMSD 
must be zero.




so the rmsd = 0.001

whereas when I use online server it gives me 1.4.

so what am I doing wrong?



Then whatever you're giving the online server is different.  The Gromacs 
calculation seems to be correct.


-Justin


regrads
anupam





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] rmsd between different monomers

[Itamar Kass]

Hi Anupam ,

To me it seems that you have used the the wrong groups for the RMSD, you
actually compare the protein to himself. Have a second look on at the
group contact, you groups should be numbered 12 or higher.


cheers,
Itamar

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au


- Original Message -
From: Anupam Nath Jha 
Date: Sunday, May 9, 2010 3:48 pm
Subject: [gmx-users] rmsd between different monomers
To: gmx-users@gromacs.org

> 
> Dear all
> 
> I made an index file with 4 different groups for 4 different chains 
> (since my
> protein is a tetramer) and then run
> 
> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
> 
> to get the rmsd between two different monomers from the same 
> structure,it asked me two different groups and I gave 0 and 1.
> 
> The output file is like this
> 
> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
> #
> # g_rms is part of G R O M A C S:
> #
> # Grunge ROck MAChoS
> #
> @title "RMSD"
> @xaxis  label "Time (ps)"
> @yaxis  label "RMSD (nm)"
> @TYPE xy
> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
>   0.0000.001
> 
> 
> so the rmsd = 0.001
> 
> whereas when I use online server it gives me 1.4.
> 
> so what am I doing wrong?
> 
> regrads
> anupam
> 
> 
> 
> -- 
> 
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
> 
> 
> 
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
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Re: [gmx-users] rmsd between different monomers

[Mark Abraham]

On 7/05/2010 7:11 PM, Anupam Nath Jha wrote:


Dear all

How can we calculate the rmsd between different monomers from of a protein. for
example I have a tetramer and I have to calculate the rmsd between chain A to B,
A to C and A to D with time.

I was trying using g_rms but couldn't do that.


g_rms does that, but we're not going to guess what you were doing wrong. 
Tell us what you did and why it didn't work like you expected it to :-)


Mark
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Re: [gmx-users] rmsd between different monomers

[Shankar Prasad Kanaujia]

There is one web-server in our lab.
http://10.188.1.15/3dss/
Use third option.

On Fri, May 7, 2010 at 2:41 PM, Anupam Nath Jha wrote:

>
> Dear all
>
> How can we calculate the rmsd between different monomers from of a protein.
> for
> example I have a tetramer and I have to calculate the rmsd between chain A
> to B,
> A to C and A to D with time.
>
> I was trying using g_rms but couldn't do that.
>
> thanks with regards
> anupam
>
>
>
> --
> Science is facts; just as houses are made of stone, so is science is made
> of
> facts; but a pile of stones is not a house, and  a collection of facts is
> not
> necessarily science.
>
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> --
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>



-- 
Yours Sincerely,
Shankar Prasad Kanaujia
Research Student
C/O - Dr. K. Sekar
Bioinformatics Centre, SERC
Indian Institute of Science, Bangalore-12
Phone - 9480258032
Office - 080-2293-3059
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Re: [gmx-users] RMSD of Different Simulations

[XAvier Periole]

g_confrms -f1 conf1.gro -f2 conf2.gro -n1 ind1.ndx -n2 ind2,ndx should  
do the trick.


On Feb 9, 2010, at 1:27 AM, Mark Abraham wrote:


On 09/02/10 10:20, V Hariharan wrote:

Hello All,

I've taken the average peptide structure from two different MD
simulations using g_rmsf.  Is there a method for calculating the RMSD
between those two structures? The only difference between the two
peptides is a single residue mutation.  Thanks.


You may need to use trjconv to strip both down to a common matching  
set of (say) CA atoms. Then g_rms -s A.gro -f B.gro.


Mark
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Re: [gmx-users] RMSD of Different Simulations

[Mark Abraham]

On 09/02/10 10:20, V Hariharan wrote:

Hello All,

I've taken the average peptide structure from two different MD
simulations using g_rmsf.  Is there a method for calculating the RMSD
between those two structures? The only difference between the two
peptides is a single residue mutation.  Thanks.


You may need to use trjconv to strip both down to a common matching set 
of (say) CA atoms. Then g_rms -s A.gro -f B.gro.


Mark
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Re: [gmx-users] rmsd value discrepancy from g_rms & g_cluster

[Justin A. Lemkul]

Segun Jung wrote:

Hello there,

I have used g_rms and g_cluster for RNA structure analysis and noticed 
that they give me different rmsd values.


For example, calculating rmsd values using the g_rms gives me a minimum 
rmsd value of 0.7nm, but using g_cluster


it gives me the minimum rmsd value of 0.3nm. Both uses the same atom 
(C3') for the rmsd calculation.


Would someone clarify this issue?



These tools don't provide a redundant function, from what I understand.  If you 
think that you're somehow using g_cluster to calculate an absolute RMSD, please 
provide the command line you're using.  My understanding of g_cluster (and my 
previous usage of it) suggests that the RMSD is somewhat relative, defining RMSD 
from a cluster member, not a single reference from, for example, the start of 
the simulation (or whatever frame you choose), as is the case with g_rms.


If you're still not convinced, post your command lines and the snippet of the 
relevant output files that are causing you concern.


-Justin



Many thanks,

Segun



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD

[Mark Abraham]

leila karami wrote:

Hi
 
I have 2 questions about rmsd calculation:
 
1) why rmsd calculation is done on heavy atoms?
 
2) what means of mass weighted superposition (rmsd is calculated after 
mass weighted superposition)


Consider the difference between centre of mass and center of geometry... 
(Wikipedia is probably your friend here!)


Mark
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Re: [gmx-users] RMSD

[Justin A. Lemkul]

On 1/10/10 3:51 AM, leila karami wrote:

Hi
I have 2 questions about rmsd calculation:
1) why rmsd calculation is done on heavy atoms?


You calculate RMSD on whatever subset of atoms you wish; you are not necessarily 
limited to heavy atoms only.



2) what means of mass weighted superposition (rmsd is calculated after
mass weighted superposition)


Sounds like some background reading is necessary :)

-Justin



Any help will highly appreciated!



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD Vs Residue no by Grace

[Itamar Kass]

Hi,

RMSD is given at a specific time, so you can ran g_rms for each residue
(create index file witha specific residue in) and then take the RMSD of each
residue at time T and plot it.

But I think you should look into g_rmsf, this might fit you better, although
it calculate the fluctuations rather that the distance.

Best,
Itamar

On Mon, Nov 30, 2009 at 1:37 AM, rituraj purohit
wrote:

> Dear friends,
> I am able to plot,  RMSD between Time (ps) by following command by using
> GRACE..
>
> g_rms -s md.tpr -f md.xtc
> xmgrace  rmsd.xvg
>
> How we can I plot a graph betwwen RMSD and residue no ..??
> My aim is to find RMSD at each residues. How i can do that?
>
> looking forward for u r important suggestions.
>
> Thanking you
>
> Regards
> Rituraj
>
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Re: [gmx-users] RMSD Vs Residue no by Grace

[Justin A. Lemkul]

rituraj purohit wrote:

Dear friends,
I am able to plot,  RMSD between Time (ps) by following command by using 
GRACE..


g_rms -s md.tpr -f md.xtc   
xmgrace  rmsd.xvg


How we can I plot a graph betwwen RMSD and residue no ..??
My aim is to find RMSD at each residues. How i can do that?


g_rmsf -res -od

-Justin



looking forward for u r important suggestions.

Thanking you

Regards
Rituraj 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RMSD of Aminoacids

[Mark Abraham]

Andy Torres wrote:
Hi, I'm trying to compare two proteins with the same number of 
aminoacids with g_confrms, and it works all right, but it gives me the 
RMSD of the hole protein, and I need the distances (or deviations) of 
each aminoacid. I know this data shoul be there, but I don't know how to 
get it (I've got the mean structure of each protein, calculated with 
g_rmsf, but this data is not fitted each other)


Have a look at g_confrms -h. Probably with the right index groups 
constructed you can fit with one group and observe the RMSD with another.


Mark
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Re: [gmx-users] rmsd

[Justin A. Lemkul]

shahrbanoo karbalaee wrote:

Dear justin
I have rmsd graph from peptide (13 amino acid).would you please tell
me about generally range of rmsd for good simulation.In my table rmsd
start from 2 nm and come up to 3 and   change  between 3  to 3.5
nm.the solvent is tfe/water.thanks for your advise.



I would argue that there is no such thing as a generalized "good" RMSD.  It is 
entirely dependent upon the stability of your protein, the solvent conditions, 
and whether or not you have appropriate simulation parameters.  Check for 
stability in the RMSD value over time, and whether or not the behavior you are 
seeing in the simulation makes sense based on what is known experimentally (if 
possible).


-Justin


best regards



--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Re: [gmx-users] rmsd on homologous protein structure

[Tatsiana Kirys]

tahnk you i'll try that

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Re: [gmx-users] rmsd on homologous protein structure

[Ran Friedman]

Hi,

For individual structures, you can use g_confrms.
If you want a trajectory you can download do_multiprot from the user
contributions section, and follow the instructions there. Note that
multiprot aligns based on the structure only (no sequence information).

Ran.

Tatsiana Kirys wrote:
> Hi,
>
> i want to calculate rmsd on homologous protein structures that have different 
> residue numbers. 
> As far as i understood g_rms gives only rmsd of the same structure in 
> different configurations, but it doesn't fit homologous protein structures? 
>
> In Option -f2 can i provide a trajectory of a homologous protein structure of 
> it also have to be a reserence structure trajectory (which is provided in -s)?
>
> many many thanks
> Tatsiana 
>   
-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
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Re: [gmx-users] rmsd on homologous protein structure

[Mark Abraham]

Tatsiana Kirys wrote:

Hi,

i want to calculate rmsd on homologous protein structures that have different residue numbers. 
As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? 


Yep.


In Option -f2 can i provide a trajectory of a homologous protein structure of 
it also have to be a reserence structure trajectory (which is provided in -s)?


You can provide anything that will allow for a meaningful 1:1 
correspondence of atomic sites. Depending how homologous these proteins 
are, you might need to use trjconv to strip out side-chains, leave only 
alpha-carbons, trim the terminal residues or such. Once you have ordered 
sets of numbers of the same size you can get a meaningful number out of 
g_rms.


Mark
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Re: [gmx-users] rmsd calculation of helix only

[Justin A. Lemkul]

ravi sharma wrote:

Hello everyone

is there any idea how can i calculate rmsd for a given helix or all 
helix in a protein from a trejectory???




Create an index group, specifying only the residues you care to analyze, and 
pass it to g_rms.


-Justin



-Ravi


Ravi Datta Sharma
Lecturer,
Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
 



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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] RMSD between

[David van der Spoel]

On Sat, 9 Aug 2008, jayant james wrote:


hi !
I am interested in plotting the RMSD between two amino acids to see if
they come close or move away during simulations.
Any suggestions would be helpful.

g_mindist


Thanks
Jayant James

--
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)





David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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Re: [gmx-users] RMSD, two simulations

[Xavier Periole]

On Thu, 26 Jun 2008 13:38:30 +0200
 Michal Kolinski <[EMAIL PROTECTED]> wrote:

Dear Users,

The closest tool to your need is g_rms using the option -m, which
generates a matrix of rmsd between all pairs of conformations
present in the trajectory.

To compare the two trajectories you should concatenate them (trjcat)
into one unique trajectory.

To overcome the problem of different chain length (which has to be
resolved before concatenating!) you can use trajectories of subset
of proteins, namely using the common part between the two topologies.
trjconv can help you doing this with an index (different for each
model).
 
Retraining your analysis to trajectories of Calphas or backbone

atoms would speed up all the calculations.
 
I've created two different models of the same 
transmembrane protein.  These two models were 
created using homology approach using two different 
templates (both with similar sequence similarity 
to the sequence of the target protein).  Next, I 
did two separate 25ns simulations of those two 
obtained protein models in water and lipid environment.  
RMSD value calculated using g_rms reaches about 3.5 A 
after 10 ns in two simulations and stays stable for 
the rest of the MD time.  

What I want to do is to obtain a plot  of  RMSD 
between those two models (model one vs model two) 
for each corresponding frame of those two MD simulations
(I just want to add that the length of protein chain is 
different in both protein models).Is there a script 
available from gromacs tools which could be used for this?  
Could you give me some sugestions how to treat this problem? 
Thank you in advance.
Michal 


-
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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Re: [gmx-users] RMSD, two simulations

[Marcus Kubitzki]

Hi Michael,

g_rms should do the trick. First create an index file having
an atom group identical in both systems. Then,
g_rms -s ref.pdb -f1 trj1.xtc -f2 trj2.xtc -m rmsd.xpm gives
you an rmsd matrix with entry ij given by
RMSD[(frame i of trj1),(frame j oftrj2)]. The diagonal of that
matrix should be what you want.

Marcus

Michal Kolinski wrote:
> Dear Users,
>  
> I've created two different models of the same
> transmembrane protein.  These two models were
> created using homology approach using two different
> templates (both with similar sequence similarity
> to the sequence of the target protein).  Next, I
> did two separate 25ns simulations of those two
> obtained protein models in water and lipid environment. 
> RMSD value calculated using g_rms reaches about 3.5 A
> after 10 ns in two simulations and stays stable for
> the rest of the MD time. 
>  
> What I want to do is to obtain a plot  of  RMSD
> between those two models (model one vs model two)
> for each corresponding frame of those two MD simulations
>  (I just want to add that the length of protein chain is
> different in both protein models).Is there a script
> available from gromacs tools which could be used for this? 
> Could you give me some sugestions how to treat this problem?
> Thank you in advance.
> Michal
> 
> 
> 
> 
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Computational Biomolecular Dynamics Group
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Re: [gmx-users] RMSD graph

[Mark Abraham]

Anamika Awasthi wrote:



Dear All,
   Please tell, what should I predict from this graph?


We can't tell from your graph what's happening because you haven't told 
us how you generated it. It's also not our job to do so - it's yours. 
You can go at look at your data at the points that have "interesting" 
behaviour and see what is causing that. We can't.



   I can understand this is normal type of graph.
   Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to 
restart this again and again, I used tpbconv for the same.


but now when I was trying to get rmsd plot from my running job..its not 
reading the tpr file, which I got from tpbconv , its reading previous 
tpr file.


It's doing what you're telling it to do. No more, no less.

If you don't tell us exactly what you were doing and what you were 
trying to do, we can't offer any insight into the failure.



Is it okey?


No. I guess wildly that you need to correct for periodicity effects, see 
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions


Mark
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Re: [gmx-users] RMSD plot

[Mark Abraham]

minnale wrote:


If I use the command in this way with option -mir insted of -o

g_rms -f 9ns.xtc -n r20-50.ndx -mir mirror.xvg -pbc -s min.gro
  selected r_20-50 for least square fit group
  selected c-alpha for RMSD calculation

if I plot a graph by using mirror.xvg file there is no fluctuations 
after 4ns to 9ns I can say system is almost stabilised, but if i use -o 
option RMSD values are quite vary and system not yet stable even at 9ns
so shall i stop the simulation or continue the simulation some more time 
as Justin said.

sorry for the asking trivial questions.
Thanks for your appreciation 



 >have you mirrored your trajectory  back to a normal box?
 >Have you inspected it visually, does it always stay inside the box?

 >If not use trjconv -pbc nojump -fit rot+trans


Florian wasn't suggesting using the "-mir" flag to g_rms, but rather to 
use trjconv.


Your results suggest that you haven't merely added the use of the "-mir" 
option, for it's not possible for a trajectory to fluctuate with respect 
to a single structure, and to be stable with respect to that structure's 
mirror image.


Mark
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Re: [gmx-users] RMSD plot

[Florian Haberl]

Hi,

On Thursday, 15. May 2008 18:04, Justin A. Lemkul wrote:
> Quoting minnale <[EMAIL PROTECTED]>:
> > Thanks for your prompt reply Justin
> > I am simulating 1ns each time, Due to this its happening? why i got this
> > doubt because at each 1ns, graph is showing either lowside fluctuations
> > or upside fluctuations.
>
> I don't understand what you mean.


have you mirrored your trajectory  back to a normal box?
Have you inspected it visually, does it always stay inside the box?

If not use trjconv -pbc nojump -fit rot+trans

greetings,

Florian




>
> I doubt that you're causing any problems by simulating 1 ns at a time.  The
> best I can guess, you just need more time for your simulation to stabilize.
>  Without any knowledge of what it is, it's hard to say.  Be aware that RMSD
> can fluctuate quite widely until the structure is happy.
>
> -Justin
>
> > Thanks for any appreciation
> >
> > On Thu, 15 May 2008 Justin A.Lemkul wrote :
> > >What you've done looks reasonable.  Depending on how unstable the RMSD
> > > is,
> >
> > you
> >
> > >may just have to simulate longer.
> > >
> > >Always remember to use a pertinent subject line when sending messages. 
> > > That
> >
> > way
> >
> > >more people are likely to respond if they see something of interest!
> > >
> > >-Justin
> > >
> > >Quoting minnale <[EMAIL PROTECTED]>:
> > > > Hi all,
> > > > I ran protein simulation in water for 9ns and plotted RMSD but it
> > > > didnt stabilize, iam doubting on steps what I have done
> > > > I am mentioning the steps
> > > >
> > > > 1.EM in vaccum
> > > > 2.PR in vaccum in NVT
> > > > 3.EM in water
> > > > 4.PR in water in NVT
> > > > 5.Production run for 250 ps in NPT remain 9ns run in MVT condition
> > > > 6. Intersected the protein residues from whole protein
> > > > so I have used
> > > > make_ndx -f protein.gro -n r_20-50.ndx
> > > >  selected  1 & r 20-50 means in whole protein select from res 20-50
> > > > 7.g_rms -f 9ns_prot.xtc -n r_20-50.ndx -pbc -s min_wat.gro -o
> > > > rms_9ns.xvg Here I have selected "protein&r_20-50" for group least
> > > > square fit and then selected " group 3(c-alpha)" for RMSD calculation
> > > >
> > > > In above mentioned steps did I do any where wrong
> > > > I am pasting my md.mdp file
> > > > title   =  dpt_prod
> > > > constraints =  hbonds
> > > > integrator  =  md
> > > > dt  =  0.002; ps !
> > > > nsteps  =  50   ; total 250 ps.
> > > > nstcomm =  1
> > > > nstxout =  100
> > > > nstlog  =  100
> > > > nstenergy   =  100
> > > > nstlist =  10
> > > > ns_type =  grid
> > > > coulombtype =  PME
> > > > rlist   =  0.9
> > > > rcoulomb=  0.9
> > > > rvdw=  1.4
> > > > pbc =  xyz
> > > > comm_grps   =  Protein
> > > > ; Berendsen temperature coupling is on in two groups
> > > > Tcoupl  =  Berendsen
> > > > tc-grps =  Protein   SoL_CL-
> > > > tau_t   =  0.1   0.1
> > > > ref_t   =  300   300
> > > > ; isotropic pressure coupling is off
> > > > Pcoupl  =  no
> > > > pcoupltype  =  isotropic
> > > > tau_p   =  0.5
> > > > compressibility =  4.5e-5
> > > > ref_p   =  1.0
> > > > ; Energy monitoring
> > > > energygrps  =  Protein  SOL_CL-
> > > > ; Generate velocites is off at 300 K.
> > > > gen_vel =  no
> > > > gen_temp=  300
> > > > gen_seed=  173529
> > > > ~
> > > >
> > > > Waiting for invaluable suggestion
> > > > Thanks in advance
> > >
> > >
> > >
> > >Justin A. Lemkul
> > >Graduate Research Assistant
> > >Department of Biochemistry
> > >Virginia Tech
> > >Blacksburg, VA
> > >[EMAIL PROTECTED] | (540) 231-9080
> > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> > >
> > >
>
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> 
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---
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 Telephone: +49(0) − 9131 − 85 26573
 Mailto: flori

Re: Re: [gmx-users] RMSD plot

[Justin A. Lemkul]

Quoting minnale <[EMAIL PROTECTED]>:

>
> Thanks for your prompt reply Justin
> I am simulating 1ns each time, Due to this its happening? why i got this
> doubt because at each 1ns, graph is showing either lowside fluctuations or
> upside fluctuations.

I don't understand what you mean.

I doubt that you're causing any problems by simulating 1 ns at a time.  The best
I can guess, you just need more time for your simulation to stabilize.  Without
any knowledge of what it is, it's hard to say.  Be aware that RMSD can
fluctuate quite widely until the structure is happy.

-Justin

> Thanks for any appreciation
>
>
>
>
> On Thu, 15 May 2008 Justin A.Lemkul wrote :
> >
> >What you've done looks reasonable.  Depending on how unstable the RMSD is,
> you
> >may just have to simulate longer.
> >
> >Always remember to use a pertinent subject line when sending messages.  That
> way
> >more people are likely to respond if they see something of interest!
> >
> >-Justin
> >
> >Quoting minnale <[EMAIL PROTECTED]>:
> >
> > >
> > > Hi all,
> > > I ran protein simulation in water for 9ns and plotted RMSD but it didnt
> > > stabilize, iam doubting on steps what I have done
> > > I am mentioning the steps
> > >
> > > 1.EM in vaccum
> > > 2.PR in vaccum in NVT
> > > 3.EM in water
> > > 4.PR in water in NVT
> > > 5.Production run for 250 ps in NPT remain 9ns run in MVT condition
> > > 6. Intersected the protein residues from whole protein
> > > so I have used
> > > make_ndx -f protein.gro -n r_20-50.ndx
> > >  selected  1 & r 20-50 means in whole protein select from res 20-50
> > > 7.g_rms -f 9ns_prot.xtc -n r_20-50.ndx -pbc -s min_wat.gro -o rms_9ns.xvg
> > >   Here I have selected "protein&r_20-50" for group least square fit and
> > >then selected " group 3(c-alpha)" for RMSD calculation
> > >
> > > In above mentioned steps did I do any where wrong
> > > I am pasting my md.mdp file
> > > title   =  dpt_prod
> > > constraints =  hbonds
> > > integrator  =  md
> > > dt  =  0.002; ps !
> > > nsteps  =  50   ; total 250 ps.
> > > nstcomm =  1
> > > nstxout =  100
> > > nstlog  =  100
> > > nstenergy   =  100
> > > nstlist =  10
> > > ns_type =  grid
> > > coulombtype =  PME
> > > rlist   =  0.9
> > > rcoulomb=  0.9
> > > rvdw=  1.4
> > > pbc =  xyz
> > > comm_grps   =  Protein
> > > ; Berendsen temperature coupling is on in two groups
> > > Tcoupl  =  Berendsen
> > > tc-grps =  Protein   SoL_CL-
> > > tau_t   =  0.1   0.1
> > > ref_t   =  300   300
> > > ; isotropic pressure coupling is off
> > > Pcoupl  =  no
> > > pcoupltype  =  isotropic
> > > tau_p   =  0.5
> > > compressibility =  4.5e-5
> > > ref_p   =  1.0
> > > ; Energy monitoring
> > > energygrps  =  Protein  SOL_CL-
> > > ; Generate velocites is off at 300 K.
> > > gen_vel =  no
> > > gen_temp=  300
> > > gen_seed=  173529
> > > ~
> > >
> > > Waiting for invaluable suggestion
> > > Thanks in advance
> > >
> >
> >
> >
> >
> >
> >Justin A. Lemkul
> >Graduate Research Assistant
> >Department of Biochemistry
> >Virginia Tech
> >Blacksburg, VA
> >[EMAIL PROTECTED] | (540) 231-9080
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> >
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] RMSD VS. parallel simulation

[Mark Abraham]

DeChang Li wrote:

Dear all,

  I used Gromacs-3.3.1 to simulate a small protein in water.
I have used 2 and 16 CPUs to do the simulation respectively. But
I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs
simulation and 0.20 nm in the 16 CPUs one. Are these differences
reasonable?


MD allows you to observe an ensemble (usually at or approaching 
equilibrium) over time. Any single point of that time isn't any more 
significant than any other.  So you should expect any pair of points in 
different simulations (which had their velocities generated with 
different random numbers, right?) to generally give different values for 
observables, and for that not to mean anything much. Distributions of 
observables over long enough periods of time should be the same, however.



  In the 16 CPUs simulation, the RMSD of protein at t=0 was about
0.1 nm, why not equal to zero? I used the initial structure for the
least squares fit.


If you've done an equilibration or EM, the structure can have changed 
during that.


Mark
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Re: [gmx-users] rmsd with average structure

[David van der Spoel]

Prasad Gajula wrote:

Dear Groamcs users,

I calcualted the average structure from the simulation trajectory. when I
calculate the rmsd of the protein to this average sturture, it is giving
average rmsd of 0.16 nm. But, it is not clear for me why the average
sturcture is never adapted rmsd near (or equal) to zero. I did not
calculate the rmsd with respect to the starting structure either.
Any clue?

the average structure is unphysical, it may have long bonds etc.


Thanks in advance!
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] rmsd fluctuation of the dihedrals

[David van der Spoel]

Prasad Gajula wrote:

Dear Gromacs users,
can some one give me a hint to calculate the " rmsd fluctuation of the
dihedrals"  to see the angle dynamcis.
compute the angles as a function of time (g_angle), then use xmgrace to 
compute the fluctuations.note that dihedrals are periodic, so averages 
and fluctuations may not make much sense. You are better of with a 
distribution (g_analyze on the results of g_angle).

thanks in advance

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Re: [gmx-users] RMSD calculations by g_rms

[Tsjerk Wassenaar]

Hi Monika, Xavier,

You can't really judge a run from the rmsd ;)

g_rms and VMD should the exact same result. You might check the reference
> frame you use and make sure you fit your protein using the same set of
> atoms.
>

I concur, and Xavier, you hit the spot with referring to the reference
frame.

> 2. I have given two consecutive 3ns runs in continuation. first for 3ns,
> > then next again for 3ns. In latter, I used unconstrained-start=yes. When
> > I am concatenating these xtc files, to get total of 6ns, and then doing
> > g_rms, I am getting a dip at 3000 and there it seems to follow earlier
> > pattern of VMD.
> > that 1 to 3000ps- values of rmsd decreases from 0.5 to 0.005 nm,
> > then 3001 to 6000ps - values of rmsd increases from 0.0698 to 0.248 nm.
>
> Check again your reference frame, and you may have made a mistake in your
> continuation run, I mean the way you actually continued it.
>

So, what happens when you get a dip in the rmsd? The structure comes close
to your reference structure. Or, the other way around, your reference
structure seems to match the structure at the break of the trajectories.
Thus, it seems that you have used the continuation run input file as the
reference frame. I think that VMD only extracts the topology from the .tpr
file and does the rmsd calculation with respect to the first set of
coordinates in the trajectory.


> > In case of alone rmsd calculations, 3ns rmsd showed increasing
> > deviations from 0.0005 to 0.509 nm.
> > 6ns run rmsd too showed increasing deviations from 0.00 to 0.248nm
>
> This does not look like a regular continuation run. But again you
> reference frame might be the problem.
>

Well, the rmsd tends to rise more during the first part of the simulation
(relaxation effects, etc). So if you then take the run input file from the
continuation run and use it to calculate the rmsd of the second part, it's
likely that you'll see less of a rise in the rmsd.


> > But when I am concatenating them, then the 3ns run showed deviations
> > down (different from its original) and 6ns showed up (similar to its
> > original).
>
> Then the reference frame is not the problem but the way you continued.
> Do you fit your protein before the rmsd calculation?
>

Au contraire, the reference is the problem (or actually cause).

>
> > I really dont know what is happening and why?? Where the things are
> > going hay-ward??
> >
>

Because of an inconsistent approach. Please think carefully about which
reference file you use where. In these cases it's best to have a
start.tpror something, which corresponds to the initial starting
structure of your
simulation, for analysis.

I hope it helps and best wishes for 2008 ;)

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] RMSD calculations by g_rms

[Xavier Periole]

On Mon, 31 Dec 2007 16:22:40 +0530
 Monika Sharma <[EMAIL PROTECTED]> wrote:
Dear All, 
I have two queries regarding the rmsd calculations of gromacs run.


1. I was trying to calculate rmsd for 3ns run of my protein system. I
did it in two ways: VMD (RMSD Traj tool) and g_rms. I found great
differences in pattern. I know that VMD gives values in angstrom,
instead g_rms gives values in pm. The thing is that in case of VMD traj
calculation, I get the rmsd values in decreasing order from around 5.5
to 0.5 angstroms. But in g_rms I get in ascending order from 0.0 to
0.5nm. And this should be the right thing (ascending order). This thing
really confuses me that why is it happening? Has anyone also encountered
such problem??
I am using xtc for VMD.


g_rms and VMD should the exact same result. You might check the reference
frame you use and make sure you fit your protein using the same set of
atoms.


2. I have given two consecutive 3ns runs in continuation. first for 3ns,
then next again for 3ns. In latter, I used unconstrained-start=yes. When
I am concatenating these xtc files, to get total of 6ns, and then doing
g_rms, I am getting a dip at 3000 and there it seems to follow earlier
pattern of VMD.
that 1 to 3000ps- values of rmsd decreases from 0.5 to 0.005 nm,
then 3001 to 6000ps - values of rmsd increases from 0.0698 to 0.248 nm.


Check again your reference frame, and you may have made a mistake in your
continuation run, I mean the way you actually continued it.


In case of alone rmsd calculations, 3ns rmsd showed increasing
deviations from 0.0005 to 0.509 nm.
6ns run rmsd too showed increasing deviations from 0.00 to 0.248nm 


This does not look like a regular continuation run. But again you
reference frame might be the problem.


But when I am concatenating them, then the 3ns run showed deviations
down (different from its original) and 6ns showed up (similar to its
original).


Then the reference frame is not the problem but the way you continued.
Do you fit your protein before the rmsd calculation?
 

I really dont know what is happening and why?? Where the things are
going hay-ward??

For g_rms, I am using backbone for least square fit and protein for rmsd
calculation. Similar pattern in all.

Any kind of suggestions are welcome..

Regards,
Monika



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-
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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Re: [gmx-users] RMSD

[Florian Haberl]

On Tuesday, 24. April 2007 20:23, Dhananjay wrote:
> Hello all,
>
> I have 10 pdb files. I want to do simulation on each of them. But before
> that I want to check RMSD of each of them with others and want to know  an
> average RMSD over all 10 srtuctures. The  pdb files are o/p of
> protein-protein docking.
>
> In this case, can I make use of programme g_rms for the RMSD calculations ?
>
> Or any other suggestion/programme please

you can also cat each file together, and than you can calculate also with 
gromacs tools (g_rms) differnet rmsd also with -m option (matrix) so you 
should have than an 10x10 matrix so also RMSD of 1 to 2, 1 to 3 ...


greetings,

florian

-- 
---
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 Computer-Chemie-Centrum   
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 Telephone: +49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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Re: [gmx-users] RMSD

[Robert Johnson]

Hi Dhanajay,
Since you don't have a trajectory (yet) and are comparing different
structures, I think the easiest thing to do would be to compute this
with VMD (www.ks.uiuc.edu/Research/vmd). You would load your PDB files
in separately, go to the TK console and type:

set struct1 [atomselect  "all"]
set struct2 [atomselect  "all"]
...

Here,   are the mol ID (given in the Main VMD window next to
each PDB file).
Then type:

measure rmsd $struct1 $struct2

Bob

On 4/24/07, Dhananjay <[EMAIL PROTECTED]> wrote:

Hello all,

I have 10 pdb files. I want to do simulation on each of them. But before
that I want to check RMSD of each of them with others and want to know  an
average RMSD over all 10 srtuctures. The  pdb files are o/p of
protein-protein docking.

In this case, can I make use of programme g_rms for the RMSD calculations ?

Or any other suggestion/programme please




--
Dhananjay C Joshi
Project Assistant
LSB, C D F D
ECIL Road, Nacharam
Hyderabad-500 076, INDIA
Tel : +91-40-27151344
Fax : +91-40-27155610
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Re: [gmx-users] RMSD of the same protein in different solvent boxes

[Ran Friedman]

Hi,

If it's the same protein you can extract the trajectories with the
coordinates of the protein only using trjconv.

Ran.

Afonso Duarte wrote:
> Hi to All,
>
> I have some simulations of the same protein in different solvents,
> with different number of atoms for each (different solvent number of
> atoms).
> I would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
>
> I have tried g_rms with the -f2 option to include the second
> trajectory, however it finishes with a fatal error because teh number
> of total atoms is different in both trajectories.
>
> Does anybody know how to solve this question? Is it possible to
> produce the rmsd matrix in a different way?
>
> Thanks in advance
>
> Afonso
>
> __
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-- 
--
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Postdoctoral Fellow
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Department of Biochemistry
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Re: [gmx-users] RMSD of the same protein in different solvent boxes

[Florian Haberl]

hi,

On Monday, 5. February 2007 11:13, Afonso Duarte wrote:
> Hi to All,
>
> I have some simulations of the same protein in different solvents, with
> different number of atoms for each (different solvent number of atoms). I
> would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
>
> I have tried g_rms with the -f2 option to include the second trajectory,
> however it finishes with a fatal error because teh number of total atoms is
> different in both trajectories.
>
> Does anybody know how to solve this question? Is it possible to produce the
> rmsd matrix in a different way?

reduce both simulations to matching atomsize, e.g. for both simulations:
make_ndx (only backbone atoms) 

trjconv ..

g_rms 

>
> Thanks in advance
>
> Afonso
>
>  __
> Fale com seus amigos  de graça com o novo Yahoo! Messenger
> http://br.messenger.yahoo.com/

greetings,

Florian

-- 
---
 Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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Re: [gmx-users] RMSD of the same protein in different solvent boxes

[Tsjerk Wassenaar]

Hi Afonso,

Try to first extract the protein from both simulations using trjconv,
or even the backbone trajectories.

Cheers,

Tsjerk

On 2/5/07, Afonso Duarte <[EMAIL PROTECTED]> wrote:

Hi to All,

I have some simulations of the same protein in different solvents, with
different number of atoms for each (different solvent number of atoms).
I would like to calculate a rmsd matrix to compar the backbone of the
different sims.

I have tried g_rms with the -f2 option to include the second trajectory,
however it finishes with a fatal error because teh number of total atoms is
different in both trajectories.

Does anybody know how to solve this question? Is it possible to produce the
rmsd matrix in a different way?

Thanks in advance

Afonso


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] RMSD

[David van der Spoel]

Dhananjay wrote:


The starting structure is a homology model. 
(If you need some more details then please tell me)


well that explains it probably, the starting structure is not a good 
protein structure. you can use the MD to tell you why the model falls apart.




force field :  GROMOS96 43a1



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] RMSD

[Dhananjay]

The starting structure is a homology model.  
(If you need some more details then please tell me)

force field :  GROMOS96 43a1 

I have not at all added or removed any ion manually. 

amount of water : using  genboc -cs ( spc216.gro ) water is added.
 Here the details are as follows 

Reading solute configuration
ecol
Containing 1791 atoms in 175 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 4x4x5 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 17280 residues
Calculating Overlap...
box_margin = 0.315
Removed 13368 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Neighborsearching with a cut-off of 0.48
Grid: 28 x 23 x 36 cells
Succesfully made neighbourlist
nri = 75512, nrj = 2292910
Checking Protein-Solvent overlap: tested 36365 pairs, removed 2592 atoms.
Checking Solvent-Solvent overlap: tested 377819 pairs, removed 4773 atoms.
Added 10369 molecules
Generated solvent containing 31107 atoms in 10369 residues
Writing generated configuration to ecolinusG_b4em.gro
ecol

Output configuration contains 32898 atoms in 10544 residues
Volume
: 341.479 (nm^3)
Density   
: 1005.02 (g/l)
Number of SOL molecules:  10369






On 8/21/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Dhananjay wrote:> Hello all,>> I am running mdrun for a system of protein having 182 residues. (Before> going for MD,  mdrun for   EM and PR  has been done as per the> instructions given in the online manual.)
>  After 3ns job is over, I calculated RMSD and it is about 0.6 nm.  This> is too high.>> In the mailing list, most of the search suggests that RMSD  may be high> depends on the system.
> One of the mails suggests to calculate RMSD domainwise. Hence I have> calculated it domainwise as the system consists of two domains. I found> that one of the domains has RMSD about 0.35 nm but the other domain is
> still showing around 0.6 nmplease give more details,amount of water,force field,ionswhere does that starting structure come frometc.>> Is there something  wrong in assigning the parameter ?
>> Please give me suggestions.>> Thanking you in advance.>> The full mdrun paramitors are as follows:>> title   =  xyz>
cpp
=  /usr/bin/cpp> constraints =  all-bonds> integrator  =  md>
dt  =  0.001;
ps !>
nsteps  =  2000
; total 20 ns> nstcomm =  1> nstxout =  500> nstvout =  1000> nstfout =  0> nstlist =  10> nstlog  =  10
> nstenergy   =  10> ns_type =  grid>
rlist  
=  0.9  ; nm> coulombtype =  PME>
rcoulomb=  0.9  ;
nm> rvdw=  1.4> fourierspacing  =  0.12> fourier_nx  =  0> fourier_ny  =  0> fourier_nz  =  0> pme_order   =  4
> ewald_rtol  =  1e-5> optimize_fft=  yes> ; Berendsen temperature coupling is on in three groups> Tcoupl  =  berendsen>
tau_t  
=  0.1  0.1> tc_grps =  protein  sol>
ref_t  
=  300  300> ; Pressure coupling is on> Pcoupl  =  berendsen> pcoupltype  =  isotropic> tau_p   =  0.5> compressibility =  4.5e-5> ref_p   =  
1.0> ; Generate velocites is on at 300 K.> gen_vel =  yes> gen_temp=  300.0> gen_seed=  173529>>> --> Dhananjay>>
> >> ___> gmx-users mailing listgmx-users@gromacs.org
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--David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Swedenphone:  46 18 471 4205  fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED]
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Re: [gmx-users] RMSD

[David van der Spoel]

Dhananjay wrote:

Hello all,

I am running mdrun for a system of protein having 182 residues. (Before 
going for MD,  mdrun for   EM and PR  has been done as per the 
instructions given in the online manual.)
 After 3ns job is over, I calculated RMSD and it is about 0.6 nm.  This 
is too high.


In the mailing list, most of the search suggests that RMSD  may be high 
depends on the system.
One of the mails suggests to calculate RMSD domainwise. Hence I have 
calculated it domainwise as the system consists of two domains. I found 
that one of the domains has RMSD about 0.35 nm but the other domain is 
still showing around 0.6 nm


please give more details,
amount of water,
force field,
ions
where does that starting structure come from
etc.

 
Is there something  wrong in assigning the parameter ?


Please give me suggestions.

Thanking you in advance.

The full mdrun paramitors are as follows:

title   =  xyz
cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
dt  =  0.001; ps !
nsteps  =  2000 ; total 20 ns
nstcomm =  1
nstxout =  500
nstvout =  1000
nstfout =  0
nstlist =  10
nstlog  =  10
nstenergy   =  10
ns_type =  grid
rlist   =  0.9  ; nm
coulombtype =  PME
rcoulomb=  0.9  ; nm
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
; Berendsen temperature coupling is on in three groups
Tcoupl  =  berendsen
tau_t   =  0.1  0.1
tc_grps =  protein  sol
ref_t   =  300  300
; Pressure coupling is on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


--
Dhananjay




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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Re: [gmx-users] RMSD for domain

[leafyoung81-group]

with an index file- Original Message From: Dhananjay <[EMAIL PROTECTED]>To: Discussion list for GROMACS users Sent: Monday, July 17, 2006 11:36:29 PMSubject: [gmx-users] RMSD for domainHello all,My protein consist of two domains. I got RMSD plot for complete system.According to the manual one can calculate RMSD for different time period by initiating initial and final time.
Will it be possible to calculate RMSD for two seperate domains(by restricting residues) of the same system over same time period?Thanking you in advance.-- Dhananjay___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php___
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Re: [gmx-users] RMSD for domain

[Xavier Periole]

My protein consist of two domains.

I got RMSD plot for complete system.

According to the manual one can calculate RMSD for different time 
period by initiating initial and final time.


Will it be possible to calculate RMSD for two seperate domains(by 
restricting residues) of the same system over same time period?


Yes, you have to generate an index using make_ndx -f protein.gro(pdb)

the use g_rms -f traj.trr(xtc) -n index.ndx and the program asks you to 
choose
a group in the index for the least square fit and for the rmsd 
calculation. You

just have to make your choice.

XAvier


--
--
Xavier Periole - Ph.D.

Dept. of Biophysical Chemistry / MD Group   
Univ. of Groningen

Nijenborgh 4
9747 AG Groningen
The Netherlands

Tel: +31-503634329
Fax: +31-503634398
email: [EMAIL PROTECTED]
web-page: http://md.chem.rug.nl/~periole
--

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