Re: [gmx-users] Protein goes out of the box

[spss4]

 - Message from Justin Lemkul  -
    Date: Tue, 25 Apr 2017 10:40:40 -0400
    From: Justin Lemkul 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein goes out of the box
      To: gmx-us...@gromacs.org


On 4/25/17 10:35 AM, sp...@iacs.res.in wrote:

Hii all,
I have simulated protein in 45% ethanol water mixture for 100ns. After
completion of the job I saw that maximum portion of my protein goes out
of
the box. Then I have done trjconv -pbc mol to the trajectory file. After
trjconv some portion of the protein is still out of the box. I want to
see
the local environment of the protein using the .gro file(last frame) but
some portion of protein is dry. How can I get the actual state of

protein

after completion of 100ns?


You may need a few iterations of trjconv to get what you want.



http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow


-Justin

--
==

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

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

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

==
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Hii Justin


Thank you so much for your reply.I am a new user of gromacs. Should I use
-pbc mol -center for my case? Is this give me the actual state of protein
after 100ns? Please correct me if I am wrong.
Thanks 

- End message from Justin Lemkul  -
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 112

[Raag Saluja]

Thank you, Justin! I will definitely try this out. However, I can't find
anyone or any paper where they have done a similar thing... Could you
please suggest which force field should be the best to try first?
On Tue, 25 Apr 2017 at 2:08 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>1. Re: HBond for F and S (Justin Lemkul) (Marcelo Dep?lo)
>2. User Defined Potentials (Ommair Ishaque)
>3. Most suitable intervals of temperature in REMD (? ?)
>4. Hbond residence time (Marcelo Dep?lo)
>5. addition of an isopeptide bond and its simulation (Raag Saluja)
>6. CG Graphene - dihedral problem/parameter (Sajjad Kavyani)
>7. Re: User Defined Potentials (Vytautas Rakeviius)
>
>
> --
>
> Message: 1
> Date: Mon, 24 Apr 2017 17:59:28 -0300
> From: Marcelo Dep?lo 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] HBond for F and S (Justin Lemkul)
> Message-ID:
> <
> cafaahpbgfznompkftowgjrepo86_wrawugstz-pkptyeb9j...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks, Justin!
>
>
> It worked just fine.
>
> I guess using a flag to include different atomtypes into the analyses would
> be a nice feature for next GROMACS versions.
>
> Cheers!
> --
> Marcelo Dep?lo Pol?to
> DSc. Cell and Molecular Biology - UFRGS (Brazil)
> Group of Structural Bioinformatics - Room 202
> Center of Biotechnology - UFRGS
> Phone: + 55 51 3308-7770
>
>
> --
>
> Message: 2
> Date: Mon, 24 Apr 2017 17:58:05 -0400
> From: Ommair Ishaque 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] User Defined Potentials
> Message-ID:
> <
> cajmqv+b-vl-gdwyikrdbwbukdz6csztuxlpfjskpcawbx+y...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I am Phd physics phd student at University of Delaware. I am using GROMACS
> for calculation of solvation energy of argon or methane in water. But Our
> water model has additional interaction terms other than already define in
> GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*
>
> And one of my senior colleagues was telling me in past, GROMACS had no
> quaternion algorithm for rigid molecules. It handles rigid molecules using
> SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
> we will be able to use it for our water model (CC-5spol) which has at least
> 25 sites. *If there is now a means of truly propagating the motion of rigid
> molecules without SHAKE/RATTLE/LINCS, this will be great.*
>
> I am looking forward for your positive reply. Thanks
>
> Ommair Ishaque
>
>
> --
>
> Message: 3
> Date: Tue, 25 Apr 2017 08:09:42 +0900
> From: ? ?   
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Most suitable intervals of temperature in REMD
> Message-ID:
> 

Re: [gmx-users] Dihedral angles Vs time (in ps)

[Quyen V. Vu]

I think to study orientation of ligand, you should choose three points
in ligand to defined a plane and then compute angle between that plane
in each frame vs the first frame( use module gangle).

I don't know whether I misunderstand your question or not.

Best regard,

Quyền
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[gmx-users] Dihedral angles Vs time (in ps)

[Neha Gupta]

Hi gromacs users,

After protein ligand simulation for 1 ns, I want to study the orientation
of the ligand molecule.

I want to plot time in ps (x-axis) and dihedral angle (of ligand) in
(y-axis) and view the corresponding structure of the ligand too.

How to do this?

Thanks,
Neha
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Re: [gmx-users] Protein goes out of the box

[Justin Lemkul]

On 4/25/17 10:35 AM, sp...@iacs.res.in wrote:

Hii all,
I have simulated protein in 45% ethanol water mixture for 100ns. After
completion of the job I saw that maximum portion of my protein goes out of
the box. Then I have done trjconv -pbc mol to the trajectory file. After
trjconv some portion of the protein is still out of the box. I want to see
the local environment of the protein using the .gro file(last frame) but
some portion of protein is dry. How can I get the actual state of protein
after completion of 100ns?


You may need a few iterations of trjconv to get what you want.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

--
==

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

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

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

==
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[gmx-users] Protein goes out of the box

[spss4]

Hii all,
I have simulated protein in 45% ethanol water mixture for 100ns. After
completion of the job I saw that maximum portion of my protein goes out of
the box. Then I have done trjconv -pbc mol to the trajectory file. After
trjconv some portion of the protein is still out of the box. I want to see
the local environment of the protein using the .gro file(last frame) but
some portion of protein is dry. How can I get the actual state of protein
after completion of 100ns?
Thanks in advance.

Sunipa Sarkar
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Re: [gmx-users] How to do an osmotic pressure calculation in Gromacs 5.1.4.

[Justin Lemkul]

On 4/25/17 10:29 AM, Miner, Jacob Carlson wrote:

Hello,


I am trying to set up a cube (LxLxL) of 2000 TIP3P waters and 72 urea molecules 
at 300 K with an adjacent cube (LxLxL) containing only water.

The aim with this system is to place a semipermeable membrane between along the 
dimension of the two LxLxL boxes (now a box of LxLx2L) so that a cosolvent particle 
that attempts to cross from one box to the other (Z displacement < 0 or Z-disp 
> L) will be pushed back by a flat-bottom potential. The water, meanwhile, should 
be allowed to transit through the entire 2L Z-dimension without any opposing force. 
Periodic boundary conditions will be present along the X and Y dimensions as well.

This was accomplished in a previous version of gromacs assembled by my 
colleagues in gromacs 4.0.7 and 4.5.5 who actually added their own pulling 
potential to the code.


As the formatting has changed, and now a flat-bottom potential is included in 
the newer versions of Gromacs, I wanted to know if anyone can explain how the 
code could be set up to allow this kind of force measurement to be conducted in 
Gromacs v5.1.4?



You can do it in 5.1.4 using a series of steps employing flat-bottom 
[position_restraints] but it is rather complex.  I suggest using the pull code 
of version 2016.3:


http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#com-pulling

You'll set two restraints, one with type "flat-bottom" and the other with 
"flat-bottom-high" and specify the atoms to which the restraint is applied along 
the z-axis.  That should be all there is to it (I have not tried this method but 
it should work; I have been doing osmotic pressure calculations in NAMD where it 
is also very easy).


-Justin

--
==

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

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

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

==
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[gmx-users] How to do an osmotic pressure calculation in Gromacs 5.1.4.

[Miner, Jacob Carlson]

Hello,


I am trying to set up a cube (LxLxL) of 2000 TIP3P waters and 72 urea molecules 
at 300 K with an adjacent cube (LxLxL) containing only water.

The aim with this system is to place a semipermeable membrane between along the 
dimension of the two LxLxL boxes (now a box of LxLx2L) so that a cosolvent 
particle that attempts to cross from one box to the other (Z displacement < 0 
or Z-disp > L) will be pushed back by a flat-bottom potential. The water, 
meanwhile, should be allowed to transit through the entire 2L Z-dimension 
without any opposing force. Periodic boundary conditions will be present along 
the X and Y dimensions as well.

This was accomplished in a previous version of gromacs assembled by my 
colleagues in gromacs 4.0.7 and 4.5.5 who actually added their own pulling 
potential to the code.


As the formatting has changed, and now a flat-bottom potential is included in 
the newer versions of Gromacs, I wanted to know if anyone can explain how the 
code could be set up to allow this kind of force measurement to be conducted in 
Gromacs v5.1.4?


Jake
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Re: [gmx-users] User Defined Potentials

[Justin Lemkul]

On 4/24/17 5:58 PM, Ommair Ishaque wrote:

Hi,

I am Phd physics phd student at University of Delaware. I am using GROMACS
for calculation of solvation energy of argon or methane in water. But Our
water model has additional interaction terms other than already define in
GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*



GROMACS allows the use of tabulated potentials so you can apply whatever 
functional form you like without having to mess with the source code.



And one of my senior colleagues was telling me in past, GROMACS had no
quaternion algorithm for rigid molecules. It handles rigid molecules using
SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
we will be able to use it for our water model (CC-5spol) which has at least
25 sites. *If there is now a means of truly propagating the motion of rigid
molecules without SHAKE/RATTLE/LINCS, this will be great.*



SHAKE, SETTLE, and LINCS are your only options in GROMACS for rigid molecules.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] addition of an isopeptide bond and its simulation

[Justin Lemkul]

On 4/25/17 12:42 AM, Raag Saluja wrote:

Hi!

 I need to study the effect of post-translational modifications on the
biophysical properties of my protein. This involves the addition of an
isopeptide bond to the primary chain of the C-terminal tail.

How may I add this isopeptide bond? And then which force field can I use to
simulate it?



Add the terminal residue as a new entity in the force field 
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) 
and choose "None" as the C-terminus when processing with pdb2gmx so additional 
patching isn't attempted on that residue.  The force field you choose depends on 
which one is most straightforward to you for doing the parametrization or that 
has been demonstrated to handle similar cases well.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

Hi,

Presumably that was discussed in the tutorial you were following. The Unix
diff tool can help with physically inspecting what is different between
those files. But really you should already know! A good rule of thumb is
not run a big calculation on expensive hardware
unless you know why you are doing it.

Mark

On Tue, 25 Apr 2017 12:13 abhisek Mondal  wrote:

> Hi,
>
> I'm going with it.
>
> I still have a question. If I reconstruct the system (stripping the solvent
> and thus making smaller box size) I need to go through NVT>NPT
> equilibrations again. This part I got it.
> The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
> will do ?
> What is the difference between running npt simulation with npt.mdp and
> npt_umbrella.mdp ?
>
> Please help me to catch up here.
>
> Thank you.
>
> On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/24/17 12:56 PM, abhisek Mondal wrote:
> >
> >> Hello,
> >>
> >> I'm using the configurations generated by pulling run to re-box >
> >> resolvate
> >>
> >>> ion addition > EM > npt_umbrella(10ns) and forward.
> >>>
> >>
> >> So, please clarify me something. Am I following correct path ? Should I
> >> have given a npt equilibration step prior to npt_umbrella step ?
> >>
> >>
> > Yes, as Mark said, you're essentially building all new simulation
> systems.
> > Since this is part of an umbrella sampling series, be sure you're getting
> > the same (or at least, very similar) number of water molecules in each
> box.
> >
> > -Justin
> >
> > Thank you.
> >>
> >> On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham  >
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> I already answered that. You're effectively starting again, so do that.
> >>>
> >>> Mark
> >>>
> >>> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <
> abhisek.m...@gmail.com>
> >>> wrote:
> >>>
> >>> Ok, I got it this time.
>  But what kind of equilibration I'm to perform on these stripped
> 
> >>> structures.
> >>>
>  Should I perform normal NPT equilibration as done before generating
>  configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c
> 
> >>> conf0.gro
> >>>
>  -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from
> tutorial
>  page) and followed by mdrun step ?
> 
> 
>  
> >>>
> >>>
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Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Hi,

I'm going with it.

I still have a question. If I reconstruct the system (stripping the solvent
and thus making smaller box size) I need to go through NVT>NPT
equilibrations again. This part I got it.
The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
will do ?
What is the difference between running npt simulation with npt.mdp and
npt_umbrella.mdp ?

Please help me to catch up here.

Thank you.

On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul  wrote:

>
>
> On 4/24/17 12:56 PM, abhisek Mondal wrote:
>
>> Hello,
>>
>> I'm using the configurations generated by pulling run to re-box >
>> resolvate
>>
>>> ion addition > EM > npt_umbrella(10ns) and forward.
>>>
>>
>> So, please clarify me something. Am I following correct path ? Should I
>> have given a npt equilibration step prior to npt_umbrella step ?
>>
>>
> Yes, as Mark said, you're essentially building all new simulation systems.
> Since this is part of an umbrella sampling series, be sure you're getting
> the same (or at least, very similar) number of water molecules in each box.
>
> -Justin
>
> Thank you.
>>
>> On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> I already answered that. You're effectively starting again, so do that.
>>>
>>> Mark
>>>
>>> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal 
>>> wrote:
>>>
>>> Ok, I got it this time.
 But what kind of equilibration I'm to perform on these stripped

>>> structures.
>>>
 Should I perform normal NPT equilibration as done before generating
 configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c

>>> conf0.gro
>>>
 -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
 page) and followed by mdrun step ?


 
>>>
>>>
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[gmx-users] dihedral problem - Coarse-grained graphene sheet

[Sajjad Kavyani]

Dear experts,
I want to simulate a graphene sheet with MARTINI force field. (In MARTINI
FF, the banzene is represented with 3 beads)
The problem I encountered with is the dihedral parameter.
I searched papers and found that the dihedral parameters for the sheet are
K=3.1, n=2 and phi =180.

The itp and the gro which I used both are in the zip-file below:

https://drive.google.com/open?id=0B8rMZ-61IzIWQS0tTTE1Qk9aM28

It is noteworthy that I tried both dihedral type
3   6.200 0.000 -6.2000.000 0.000 0.000
and
1 180.00   3.1  2

but the forces are high because of the parameters at the end of EM runs.

Could you please help me how to place the parameter in the topology? and
what should order of indices be? Is they correct at all?

Regards
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Re: [gmx-users] User Defined Potentials

[Vytautas Rakeviius]

Inside GROMACS folder go share/top/ you will find folders for force fileds like 
gromos53a5.ff/ there are files with water topology like tip3p.itp you can write 
your own using them as examples.
 

On Tuesday, April 25, 2017 12:58 AM, Ommair Ishaque  wrote:
 

 Hi,

I am Phd physics phd student at University of Delaware. I am using GROMACS
for calculation of solvation energy of argon or methane in water. But Our
water model has additional interaction terms other than already define in
GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*

And one of my senior colleagues was telling me in past, GROMACS had no
quaternion algorithm for rigid molecules. It handles rigid molecules using
SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
we will be able to use it for our water model (CC-5spol) which has at least
25 sites. *If there is now a means of truly propagating the motion of rigid
molecules without SHAKE/RATTLE/LINCS, this will be great.*

I am looking forward for your positive reply. Thanks

Ommair Ishaque
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[gmx-users] CG Graphene - dihedral problem/parameter

[Sajjad Kavyani]

Dear experts,
I want to simulate a graphene sheet with MARTINI force field. (In MARTINI
FF, the banzene is represented with 3 beads)
The problem I encountered with is the dihedral parameter.
I searched papers and found that the dihedral parameters for the sheet are
K=3.1, n=2 and phi =180. just that

The parameter (itp) and the gro I used is in the zip-file below:

https://drive.google.com/open?id=0B8rMZ-61IzIWQS0tTTE1Qk9aM28

It is noteworthy that I tried both dihedral type
3   4.000 0.000 -4.0000.000 0.000 0.000
and
1 180.00   2.0  2

but in every EM run, the forces are high.

Could you please help me how to place the parameter in the topology? and
what should order of indices be? Is they correct?

Regards
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