Re: [gmx-users] partial atomic charges

[Mark Abraham]

On 4/10/2011 5:20 PM, MARY VARUGHESE wrote:

Hi,

I , am working on interaction between proteins/nucleic acids and ligands.
On deriving partial atomic charges using gaussian can anyone suggest,
among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to 
suggest) and why?
I mean to get the partial atomic charges of the ligand which i have to 
dock to a protein, which charge derivation method is ideal for gromacs.


Your suggestions will be very much helpful.



The standard advice for parametrization can be found here 
http://www.gromacs.org/Documentation/How-tos/Parameterization


Mark
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[gmx-users] partial atomic charges

[MARY VARUGHESE]

Hi,



I , am working on interaction between proteins/nucleic acids and ligands. 

On deriving partial atomic charges using gaussian can anyone suggest,

among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to suggest) 
and why?

I mean to get the partial atomic charges of the ligand which i have to dock to 
a protein, which charge derivation method is ideal for gromacs.



Your suggestions will be very much helpful.



Thanking you



Mary Varughese

SPAP

M.G.University-- 
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Re: [gmx-users] MD with membrane protein

[lina]

On Tue, Oct 4, 2011 at 2:57 AM, elisa carli  wrote:

> Hi Lisa
>
Thank you very much for your reply.
> After minimimization could I run a molecular dynamic production?
> Or have I to do other sets?
>
Yes, after energy minimization, you need do some other sets (like NVT and
NPT).

Could you write me which are the commands to execute up to MD run?
>

The links Justin provided are very useful. It's not a bad idea to do some
tutor to be familiar with those procedures.


>
> Bests
>
> 2011/9/22 lina 
>
>>  On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:
>>
>>> Dear All
>>>
>>> I'd like to perfom a MD simulation on a membrane protein using DLPC or
>>> DPPC system
>>> I've downloaded the API package from this link
>>> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>>>
>>> DPPC.zip and DLPC.zip by schiu
>>>
>>> How can I use them? Where can I get a tutorial or commands illustrating
>>> the use of these packages?
>>>
>>> Thanks in advance
>>>
>>  Here is a rough procedure:
>>
>> http://www.nanoconductor.org/43A1-S3/
>>
>> Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide from
>> the gromacs tutorial (it's a bad choice to put it in the dppc, but we just
>> try it).
>>
>> pdb2gmx_g -f speptide.pdb -o speptide.gro
>>
>> choose
>> 9: GROMOS96 43a1 force field
>> 1: SPCsimple point charge, recommended
>>
>> $ tail -1 dppc.gro
>>5.68585   5.60685   6.85739
>>
>> To be as simple as possible here, we use the dimension of the dppc.gro
>>
>> editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2
>> -box  5.68585   5.60685   6.85739
>>
>> now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by
>>
>> genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top
>>
>>
>> Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,
>>
>> the purpose of doing a simple energy minimization here just want to "test"
>> the topol.top.
>>
>> it used 43A1-S3 force field (You can download from
>> http://www.nanoconductor.org/43A1-S3/).
>>
>> The head of topol.top:
>> ; Include forcefield parameters
>> #include "ffG43A1-S3.itp"
>> #include "lipids_43A1-S3.itp"
>>
>> The tail of topol.top:
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein 1
>> DPPC 71
>> SOL  3205
>>
>> I manually added DPPC  71.
>>
>> please copy the  lipids_43A1-S3.itpffG43A1-S3.itp
>> ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current
>> directory,
>> extra copy ff_dum.itp from
>> some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working
>> directory.
>>
>> I attached all those files in try.tar.gz
>>
>> https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
>>
>> mdrun_g -v -deffnm em
>>
>> works well.
>>
>>
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>>
>
>
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-- 
Best Regards,

lina
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RE: [gmx-users] Free Energy Question

[Emanuel Birru]

I think using Perturbation method is more appropriate for this kind of free 
energy calculation. Check Leach, Molecular Modelling Principle and Applications 
pp 554-568. Its clearly described there and you can implement it in GROMACS.

Cheers,
Emanuel







=
Emanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.bi...@monash.edu 
www.pharm.monash.edu.au

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Fabian Casteblanco
Sent: Tuesday, 4 October 2011 6:28 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Free Energy Question

Hello all,

I have a general question about calculating free energies.  I recently
used g_bar to calculate the free energies of decoupling coulombic and
vdW forces of a solute molecule in solvent.  I now need to calculate
the free energy of a solute molecule mutating to a new molecule
(identical but with an extra -CH3 group) in a vacuum and in a solvent.
 Does anybody know if it would be better to use g_Bar again but this
time having the extra -CH3 group completely decoupled by itself or
with it be better to use the older slow-growth method that the Gromacs
Manual talks about in Sec 3.12.  I'm not sure if there is a way to
only decouple a certain part of a molecule using the g_bar method,
rather than decoupling the entire molecule.


Thanks for your help.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] heteroatom not to be a ligand

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is 
heteroatom, it is not a ligand.
I think I shouldn't use a way as Justin tutorial 5. Because X is not a 
ligand. what should I do?




If it's not relevant to the dynamics (as is often the case with unnatural 
compounds in crystal structures), you can probably delete it.  The structure may 
require extensive equilibration to combat any artifacts of its removal.


-Justin

--


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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[gmx-users] heteroatom not to be a ligand

[ahmet yıldırım]

Dear users,

I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is
heteroatom, it is not a ligand.
I think I shouldn't use a way as Justin tutorial 5. Because X is not a
ligand. what should I do?

Thanks

-- 
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
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> Support/Mailing_Lists/Searchbefore
>  posting!
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>



-- 
Ahmet YILDIRIM
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[gmx-users] Free Energy Question

[Fabian Casteblanco]

Hello all,

I have a general question about calculating free energies.  I recently
used g_bar to calculate the free energies of decoupling coulombic and
vdW forces of a solute molecule in solvent.  I now need to calculate
the free energy of a solute molecule mutating to a new molecule
(identical but with an extra -CH3 group) in a vacuum and in a solvent.
 Does anybody know if it would be better to use g_Bar again but this
time having the extra -CH3 group completely decoupled by itself or
with it be better to use the older slow-growth method that the Gromacs
Manual talks about in Sec 3.12.  I'm not sure if there is a way to
only decouple a certain part of a molecule using the g_bar method,
rather than decoupling the entire molecule.

Thanks for your help.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
--
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Re: [gmx-users] MD with membrane protein

[Justin A. Lemkul]

elisa carli wrote:

Hi Lisa
 
Thank you very much for your reply.

After minimimization could I run a molecular dynamic production?
Or have I to do other sets?
Could you write me which are the commands to execute up to MD run?
 


http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

There is also a membrane protein tutorial linked from

http://www.gromacs.org/Documentation/Tutorials

The approach is slightly different from what has been posted before, but perhaps 
it will be of some use.


-Justin


Bests

2011/9/22 lina mailto:lina.lastn...@gmail.com>>

On Thu, Sep 22, 2011 at 11:34 AM, elisa carli
mailto:elisacarl...@gmail.com>> wrote:

Dear All
 
I'd like to perfom a MD simulation on a membrane protein using

DLPC or DPPC system
I've downloaded the API package from this link
http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
 
DPPC.zip and DLPC.zip by schiu
 
How can I use them? Where can I get a tutorial or commands

illustrating the use of these packages?
 
Thanks in advance


 Here is a rough procedure:

http://www.nanoconductor.org/43A1-S3/

Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide
from the gromacs tutorial (it's a bad choice to put it in the dppc,
but we just try it).

pdb2gmx_g -f speptide.pdb -o speptide.gro

choose
9: GROMOS96 43a1 force field
1: SPCsimple point charge, recommended

$ tail -1 dppc.gro
   5.68585   5.60685   6.85739

To be as simple as possible here, we use the dimension of the dppc.gro

editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5
4.2  -box  5.68585   5.60685   6.85739
 
now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by


genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top


Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,

the purpose of doing a simple energy minimization here just want to
"test" the topol.top.

it used 43A1-S3 force field (You can download from
http://www.nanoconductor.org/43A1-S3/).

The head of topol.top:
; Include forcefield parameters
#include "ffG43A1-S3.itp"
#include "lipids_43A1-S3.itp"

The tail of topol.top:

[ molecules ]
; Compound#mols
Protein 1
DPPC 71
SOL  3205

I manually added DPPC  71.

please copy the  lipids_43A1-S3.itpffG43A1-S3.itp   
ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into

current directory,
extra copy ff_dum.itp from 
some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current

working directory.

I attached all those files in try.tar.gz

https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB



mdrun_g -v -deffnm em

works well.


-- 
Best Regards,


lina



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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] MD with membrane protein

[elisa carli]

Hi Lisa

Thank you very much for your reply.
After minimimization could I run a molecular dynamic production?
Or have I to do other sets?
Could you write me which are the commands to execute up to MD run?

Bests

2011/9/22 lina 

>  On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:
>
>> Dear All
>>
>> I'd like to perfom a MD simulation on a membrane protein using DLPC or
>> DPPC system
>> I've downloaded the API package from this link
>> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>>
>> DPPC.zip and DLPC.zip by schiu
>>
>> How can I use them? Where can I get a tutorial or commands illustrating
>> the use of these packages?
>>
>> Thanks in advance
>>
>  Here is a rough procedure:
>
> http://www.nanoconductor.org/43A1-S3/
>
> Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide from
> the gromacs tutorial (it's a bad choice to put it in the dppc, but we just
> try it).
>
> pdb2gmx_g -f speptide.pdb -o speptide.gro
>
> choose
> 9: GROMOS96 43a1 force field
> 1: SPCsimple point charge, recommended
>
> $ tail -1 dppc.gro
>5.68585   5.60685   6.85739
>
> To be as simple as possible here, we use the dimension of the dppc.gro
>
> editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2
> -box  5.68585   5.60685   6.85739
>
> now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by
>
> genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top
>
>
> Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,
>
> the purpose of doing a simple energy minimization here just want to "test"
> the topol.top.
>
> it used 43A1-S3 force field (You can download from
> http://www.nanoconductor.org/43A1-S3/).
>
> The head of topol.top:
> ; Include forcefield parameters
> #include "ffG43A1-S3.itp"
> #include "lipids_43A1-S3.itp"
>
> The tail of topol.top:
>
> [ molecules ]
> ; Compound#mols
> Protein 1
> DPPC 71
> SOL  3205
>
> I manually added DPPC  71.
>
> please copy the  lipids_43A1-S3.itpffG43A1-S3.itp
> ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current
> directory,
> extra copy ff_dum.itp from
> some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working
> directory.
>
> I attached all those files in try.tar.gz
>
> https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
>
> mdrun_g -v -deffnm em
>
> works well.
>
>
> --
> Best Regards,
>
> lina
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] pull code problem: between protofilaments

[Shilpi Chaurasia]

Dear Chris,

Thank a lot for your reply. I am trying the pull code that you have suggested. 
And I would be more specific about the problem and code in my future mails.

regards,
Shilpi 

On 02/10/11, chris.ne...@utoronto.ca wrote:
> Dear Shilpi:
> 
> Can you use something like this?
> 
> pull = umbrella
> pull_geometry    = position
> pull_dim = N N Y
> pull_vec1    = 0 0 0
> pull_start   = no
> pull_ngroups = 1
> pull_group0  = PRO-1
> pull_pbcatom0    = 
> pull_group1  = PRO-2
> pull_pbcatom1    = 
> pull_init1   = 0 0 
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_nstxout = 500
> pull_nstfout = 500
> 
> The above is for umbrella sampling. If you want to do continuous pulling, 
> then:
> 
> pull_start   = yes
> pull_rate1   = 
> 
> ### Also:
> 
> Next time you post, please provide more specifics. For example, I suggested a 
> .mdp file in specifics to you above and I bet it would have been harder for 
> you to guess what I meant if I had just told you the general idea instead of 
> pasting some .mdp options. Likewise, your initial post would have been 
> clearer it you had copied and pasted the .mdp pull code section that you 
> tried to use.
> 
> Chris.
> 
> -- original message --
> 
> 
> Dear Gmx users,
> 
> I am
> studying the interaction between the tubulin protofilaments arranged
>  in parallel. For this operation, I have considered a tetramer and a dimer 
> from two protofilaments
> respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in
> PRO-2. I want to
>  move the dimer of PRO-2 over the tetramer of PRO-1 along the length of
> protofilaments in one axis only, keeping the PRO-1 fixed to its original
> position. I tried by assuming tetramer as 'reference group' and the
> dimer as 'pull group' in pull code but the system crashed.
> 
> I have
> succeeded in separating two dimers in Z-axis by using
> 'distance' geometry. But this case is quite different, as the pulling is
>  not face-to-face but rather a sliding movement over another
> protofilament. Here, the COM distance between the pull group (dimer of
> PRO-2) and reference group (tetramer of PRO-1) first decreases and then 
> increases while it moves. How can I simulate this operation by using pull 
> code?
> 
> Thanks,
> 
> best regards,
> Shilpi Chaurasia
> 
> 
> -- 
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Re: [gmx-users] make_ndx and rdf

[Justin A. Lemkul]

oguz gurbulak wrote:

Dear Justin,

Of course I tried  typing "help" at the make_ndx prompt but I couldn't 
generate a .ndx file for my purposes.  I strongly need expert help for 


OK, you didn't say that.  You said you tried the mailing list, manual, and the 
wiki was unavailable.  The "help" prompt is the best option.  If you don't state 
everything you tried, I'm going to go with the remaining option(s) :)


using make_ndx tool. I'm trying to generate .ndx file for more than one 
week. Finally I decided to ask it to mailing list. So I will be 
appreciate for any help.




For example, water oxygens (assuming SOL is group 2, as you said)

2 & a OW

Water hydrogens

2 & a H*

All carbon atoms in group 1

1 & a C*

-Justin


Thanks for your help.




*From:* Justin A. Lemkul 
*To:* Molecular Dynamics ; Discussion list 
for GROMACS users 

*Sent:* Monday, October 3, 2011 5:17 PM
*Subject:* Re: [gmx-users] make_ndx and rdf



Molecular Dynamics wrote:
 > Dear All,
 >
 > I want to calculate rdf for carbon-oxygen, carbon-hydrogen and 
carbon-water using g_rdf but how can I generate an .ndx file that are 
suitable for these systems ? I searched mailing list and read manual but 
couldn't generate .ndx file using make_ndx tool. However, I tried to see 
the make_ndx examples in gromacs wiki page but couldn't reach the wiki 
page. Could you please help me about generating .ndx file  ?

 >
 > Carbon in group 1
 > hydrogen in group 2
 > oxygen in group 2
 > group 2 is water
 >
 > I will be gratefull for your helps.
 >

Have you tried typing "help" at the make_ndx prompt?  You'll get tons of 
information, including the commands needed to create the groups you want.


-Justin

-- 

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] make_ndx and rdf

[oguz gurbulak]

Dear Justin,

Of course I tried  typing "help" at the make_ndx prompt but I couldn't generate 
a .ndx file for my purposes.  I strongly need expert help for using make_ndx 
tool. I'm trying to generate .ndx file for more than one week. Finally I 
decided to ask it to mailing list. So I will be appreciate for any help.


Thanks for your help.





From: Justin A. Lemkul 
To: Molecular Dynamics ; Discussion list for 
GROMACS users 
Sent: Monday, October 3, 2011 5:17 PM
Subject: Re: [gmx-users] make_ndx and rdf



Molecular Dynamics wrote:
> Dear All,
> 
> I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water 
> using g_rdf but how can I generate an .ndx file that are suitable for these 
> systems ? I searched mailing list and read manual but couldn't generate .ndx 
> file using make_ndx tool. However, I tried to see the make_ndx examples in 
> gromacs wiki page but couldn't reach the wiki page. Could you please help me 
> about generating .ndx file  ?
> 
> Carbon in group 1
> hydrogen in group 2
> oxygen in group 2
> group 2 is water
> 
> I will be gratefull for your helps.
> 

Have you tried typing "help" at the make_ndx prompt?  You'll get tons of 
information, including the commands needed to create the groups you want.

-Justin

-- 

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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[gmx-users] About the GROMOS96 parameters files

[intra\sa175950]

Shame on me!! 

Indeed, you are right Justin.  I have misread the paper. I don't know why I
cited GROMOS96. Sorry all for wasting your time with these silly questions. 

Stephane


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Re: [gmx-users] make_ndx and rdf

[Justin A. Lemkul]

Molecular Dynamics wrote:

Dear All,

I want to calculate rdf for carbon-oxygen, carbon-hydrogen and 
carbon-water using g_rdf but how can I generate an .ndx file that are 
suitable for these systems ? I searched mailing list and read manual but 
couldn't generate .ndx file using make_ndx tool. However, I tried to see 
the make_ndx examples in gromacs wiki page but couldn't reach the wiki 
page. Could you please help me about generating .ndx file  ?


Carbon in group 1
hydrogen in group 2
oxygen in group 2
group 2 is water

I will be gratefull for your helps.



Have you tried typing "help" at the make_ndx prompt?  You'll get tons of 
information, including the commands needed to create the groups you want.


-Justin

--


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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[gmx-users] make_ndx and rdf

[Molecular Dynamics]

Dear All,

I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water 
using g_rdf but how can I generate an .ndx file that are suitable for these 
systems ? I searched mailing list and read manual but couldn't generate .ndx 
file using make_ndx tool. However, I tried to see the make_ndx examples in 
gromacs wiki page but couldn't reach the wiki page. Could you please help me 
about generating .ndx file  ? 

Carbon in group 1
hydrogen in group 2
oxygen in group 2
group 2 is water

I will be gratefull for your helps. 

All the best.-- 
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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[gmx-users] RE:How to change the screen's output frequency?

[chris . neale]

Speaking of which, I think that all programs should by default list  
-hidden when they are run with -h so that users are aware that there  
are hidden options and know how to access them. The -h output could  
clearly indicate that such options are not fully tested, etc.


Chris.

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 3 15:56:45 CEST 2011

* Previous message: [gmx-users] RE:How to change the screen's  
output frequency?

* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

?? wrote:

On 2011-10-02 17:14, ?? wrote:

How to change the screen's output frequency?

ol 0.85  imb F  6% step 4188000, remaining runtime:   174 s
vol 0.87  imb F  3% step 4188100, remaining runtime:   174 s
vol 0.86  imb F  1% step 4188200, remaining runtime:   174 s
vol 0.86  imb F  4% step 4188300, remaining runtime:   174 s
vol 0.88  imb F  6% step 4188400, remaining runtime:   174 s
vol 0.87  imb F  3% step 4188500, remaining runtime:   174 s
vol 0.88  imb F  8% step 4188600, remaining runtime:   174 s
vol 0.88  imb F  6% step 4188700, remaining runtime:   174 s
vol 0.86  imb F  3% step 4188800, remaining runtime:   174 s
vol 0.87  imb F  4% step 4188900, remaining runtime:   174 s
vol 0.86  imb F  1% step 4189000, remaining runtime:   174 s
vol 0.86  imb F  5% step 4189100, remaining runtime:   174 s
vol 0.87  imb F  4% step 4189200, remaining runtime:   173 s
vol 0.88  imb F  6% step 4189300, remaining runtime:   173 s
vol 0.85  imb F  1% step 4189400, remaining


mdrun -h

I have done that ,but i did not fing the option!



The option is hidden, try mdrun -h -hidden.  You can use the -stepout  
option to

set the output frequency.  Or, you can turn off -v altogether.

-Justin


The following are the  mdrun's  options .


Option Filename  Type Description

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -o   traj.trr  Output   Full precision trajectory: trr trj cpt
  -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -cconfout.gro  Output   Structure file: gro g96 pdb etc.
  -e   ener.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file

Option   Type   Value   Description
--
-[no]h   bool   yes Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or  
cartesian

-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no or yes
-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-gcomint-1  Global communication frequency
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce  real   -1  Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility
-cpt real   1

Re: [gmx-users] RE:How to change the screen's output frequency?

[Justin A. Lemkul]

杜波 wrote:

On 2011-10-02 17:14, 杜波 wrote:

How to change the screen's output frequency?

ol 0.85  imb F  6% step 4188000, remaining runtime:   174 s
vol 0.87  imb F  3% step 4188100, remaining runtime:   174 s
vol 0.86  imb F  1% step 4188200, remaining runtime:   174 s
vol 0.86  imb F  4% step 4188300, remaining runtime:   174 s
vol 0.88  imb F  6% step 4188400, remaining runtime:   174 s
vol 0.87  imb F  3% step 4188500, remaining runtime:   174 s
vol 0.88  imb F  8% step 4188600, remaining runtime:   174 s
vol 0.88  imb F  6% step 4188700, remaining runtime:   174 s
vol 0.86  imb F  3% step 4188800, remaining runtime:   174 s
vol 0.87  imb F  4% step 4188900, remaining runtime:   174 s
vol 0.86  imb F  1% step 4189000, remaining runtime:   174 s
vol 0.86  imb F  5% step 4189100, remaining runtime:   174 s
vol 0.87  imb F  4% step 4189200, remaining runtime:   173 s
vol 0.88  imb F  6% step 4189300, remaining runtime:   173 s
vol 0.85  imb F  1% step 4189400, remaining


mdrun -h

I have done that ,but i did not fing the option!



The option is hidden, try mdrun -h -hidden.  You can use the -stepout option to 
set the output frequency.  Or, you can turn off -v altogether.


-Justin


The following are the  mdrun's  options .


Option Filename  Type Description

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -o   traj.trr  Output   Full precision trajectory: trr trj cpt
  -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -cconfout.gro  Output   Structure file: gro g96 pdb etc.
  -e   ener.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file

Option   Type   Value   Description
--
-[no]h   bool   yes Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no or yes
-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-gcomint-1  Global communication frequency
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce  real   -1  Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility
-cpt real   15  Checkpoint interval (minutes)
-[no]cpnum   bool   no  Keep and number checkpoint files
-[no]append  bool   yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxhreal   -1  Terminate after 0.99 times this time (hours)
-multi   int0   Do multiple simulations in parallel
-replex  int0   Attempt replica exchange every # 

[gmx-users] RE:How to change the screen's output frequency?

[杜波]

On 2011-10-02 17:14, 杜波 wrote:
> How to change the screen's output frequency?
>
> ol 0.85  imb F  6% step 4188000, remaining runtime:   174 s
> vol 0.87  imb F  3% step 4188100, remaining runtime:   174 s
> vol 0.86  imb F  1% step 4188200, remaining runtime:   174 s
> vol 0.86  imb F  4% step 4188300, remaining runtime:   174 s
> vol 0.88  imb F  6% step 4188400, remaining runtime:   174 s
> vol 0.87  imb F  3% step 4188500, remaining runtime:   174 s
> vol 0.88  imb F  8% step 4188600, remaining runtime:   174 s
> vol 0.88  imb F  6% step 4188700, remaining runtime:   174 s
> vol 0.86  imb F  3% step 4188800, remaining runtime:   174 s
> vol 0.87  imb F  4% step 4188900, remaining runtime:   174 s
> vol 0.86  imb F  1% step 4189000, remaining runtime:   174 s
> vol 0.86  imb F  5% step 4189100, remaining runtime:   174 s
> vol 0.87  imb F  4% step 4189200, remaining runtime:   173 s
> vol 0.88  imb F  6% step 4189300, remaining runtime:   173 s
> vol 0.85  imb F  1% step 4189400, remaining
>
mdrun -h

I have done that ,but i did not fing the option!

The following are the  mdrun's  options .


Option Filename  Type Description

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -o   traj.trr  Output   Full precision trajectory: trr trj cpt
  -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -cconfout.gro  Output   Structure file: gro g96 pdb etc.
  -e   ener.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file

Option   Type   Value   Description
--
-[no]h   bool   yes Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no or yes
-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-gcomint-1  Global communication frequency
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce  real   -1  Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility
-cpt real   15  Checkpoint interval (minutes)
-[no]cpnum   bool   no  Keep and number checkpoint files
-[no]append  bool   yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxhreal   -1  Terminate after 0.99 times this time (hours)
-multi   int0   Do multiple simulations in parallel
-replex  int0   Attempt replica exchange every # steps
-reseed  int-1  Seed for replica exchange, -1 is generate a seed
-[no]ionize  bool   no  Do a simulation including the

Re: [gmx-users] Regarding 1-d free energy profile from g_sham

[Justin A. Lemkul]

bipin singh wrote:


Thanks for your reply.
I have attached two figures here.

The first figure 1d_fel is, what I am trying to get through g_sham and 
the second figure 1d_fel_sham is what I got from g_sham.
The bindex.ndx file contains the frame indices for each bins.Now the 
problem is how to transform or determine the

exact PC's values from these frame indices.
Please provide your suggestions.


The only thing I can think to do would be to adjust the bin width with g_sham 
-bw to try to narrow down which values fall where, but I don't know if that will 
negatively impact any of the calculations.  In any case, you'll have to 
determine which values fall into which bins to make the plot that you want. 
This will likely require modifying the g_sham code or some scripting to 
post-process the output.


-Justin

On Mon, Oct 3, 2011 at 17:45, Justin A. Lemkul > wrote:




bipin singh wrote:


Hello,

I am using g_sham to plot a one dimensional free energy profile
for a given reaction coordinate( in my case it is first principal
component(PC1) from a principal component analysis). It gives me
the bin index Vs free energy plot, but I want PC's value
Vs free energy plot. Please suggest me whether it is possible
through g_sham or not.



Doubtful.  g_sham creates free energy surfaces, which are inherently
2D.  I don't think you can get it to calculate the free energy of a
given PC value, although from the free energy vs. bin plot you can
probably determine something close.  The bindex.ndx file should
contain some information that can be used to translate the bin to
the values contained within, since it's all derived from a histogram.

-Justin

-- 
==__==


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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--
---
/Regards,/
Bipin Singh






--


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] Regarding 1-d free energy profile from g_sham

[Justin A. Lemkul]

bipin singh wrote:


Hello,

I am using g_sham to plot a one dimensional free energy profile for a 
given reaction coordinate( in my case it is first principal
component(PC1) from a principal component analysis). It gives me the bin 
index Vs free energy plot, but I want PC's value
Vs free energy plot. Please suggest me whether it is possible through 
g_sham or not.





Doubtful.  g_sham creates free energy surfaces, which are inherently 2D.  I 
don't think you can get it to calculate the free energy of a given PC value, 
although from the free energy vs. bin plot you can probably determine something 
close.  The bindex.ndx file should contain some information that can be used to 
translate the bin to the values contained within, since it's all derived from a 
histogram.


-Justin

--


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] About the GROMOS96 parameters files

[Justin A. Lemkul]

intra\sa175950 wrote:
Dear GMXusers, 
 
I would like to reproduce the results obtained in the paper of Marrink et al

"Molecular dynamics simulations of the kinetics of spontaneous micelle
formation". J. Phys. Chem. B, 104:12165-12173, 2000". In this (old but
interesting) work, the authors used the GROMOS96 force field to model the
DPC lipid. I have found the topology file for the lipid in the P. Tieleman's
website but not the GROMOS96 lipid parameters. I have contacted one of the
authors (SJ Marrink), but unfortunately, he has not kept the files.  



The parameters used were not GROMOS96.  See ref. 14 in the paper cited (which 
then leads to ref. 23 of that paper).  There was a custom lipid force field 
developed for those studies.



Does anyone know where I can find this file in the GROMACS format?



Perhaps one of the original authors of the original reference can help you.


I have also found a "ffgmx_lipids.tar.gz" file in the "user contribution"
section of the GROMACS's website. Is this file is the GROMOS96 parameter for
lipids used in this paper above? 



No.  "ffgmx" refers to the long-since deprecated GROMOS87 force field with other 
ad hoc changes.  See the manual.


-Justin

--


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 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] analyzing protein conformation stability

[Mark Abraham]

On 03/10/11, *Sajad Ahrari *  wrote:


Hello Dear users
is there any command in gromacs for analysis of protein stability? or 
I should be using those related to calculation of B-factor?




That's an extremely complex thing to attempt to measure. The observables 
in MD simulations are the positions and velocities of atoms. It is 
infeasible to simulate for long enough to measure something like the 
free energy of folding. You might be able to measure a relative 
stability using alchemical free energy methods, but that's not exactly a 
beginner topic.


Mark



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[gmx-users] RMSD bonds and angles

[ahmet yıldırım]

Dear users,

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

Thanks in advance

-- 
Ahmet YILDIRIM
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[gmx-users] Regarding 1-d free energy profile from g_sham

[bipin singh]

Hello,

I am using g_sham to plot a one dimensional free energy profile for a given
reaction coordinate( in my case it is first principal
component(PC1) from a principal component analysis). It gives me the bin
index Vs free energy plot, but I want PC's value
Vs free energy plot. Please suggest me whether it is possible through g_sham
or not.



-- 
---
*Thanks and Regards,*
Bipin Singh




-- 
---
*Regards,*
Bipin Singh
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[gmx-users] analyzing protein conformation stability

[Sajad Ahrari]

Hello Dear users
is there any command in gromacs for analysis of protein stability? or I should 
be using those related to calculation of B-factor?
best regards,
sajad-- 
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[gmx-users] About the GROMOS96 parameters files

[intra\sa175950]

Dear GMXusers, 
 
I would like to reproduce the results obtained in the paper of Marrink et al
"Molecular dynamics simulations of the kinetics of spontaneous micelle
formation". J. Phys. Chem. B, 104:12165-12173, 2000". In this (old but
interesting) work, the authors used the GROMOS96 force field to model the
DPC lipid. I have found the topology file for the lipid in the P. Tieleman's
website but not the GROMOS96 lipid parameters. I have contacted one of the
authors (SJ Marrink), but unfortunately, he has not kept the files.  

Does anyone know where I can find this file in the GROMACS format?

I have also found a "ffgmx_lipids.tar.gz" file in the "user contribution"
section of the GROMACS's website. Is this file is the GROMOS96 parameter for
lipids used in this paper above? 

Thanks in advance for your response.

Stéphane 


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