[gmx-users] Effect of compilers loaded at runtime

[Dries Van Rompaey]

Hi,

I'm wondering if the version of the intel toolchain loaded when calling
mdrun affects results? My gromacs version was compiled with intel/2015b -
would it matter if module intel/2016b was loaded at runtime?

Thanks

Dries
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[gmx-users] modeling CNT, center of mass velocity, energy minimization

[mohammad r]

Hi GROMACS users,


 
I have some questions:


 
1-  Can I model a carbonnanotube (CNT) conveying fluid in GROMACS 
subjected to a magnetic field?

2-  How can I check the centerof mass velocity of my system?

3-  I want to calculate volumeand water self diffusion coefficient for 
1ns, can the energy minimizationprocess do it? Or the equilibrium processes can 
do it? I want to draw theparameters versus time.


 
Thank you, Mohammad.

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Re: [gmx-users] umbrella simulation PMF curve

[Sarath Chandra]

Your umbrellas are not well spaced. There is a gap at 1.2, 2.25 and around
4.4 which is affecting your pmf profile.

Add more simulations at those points and re-check again.

Regards,

Sarath

On 22 February 2016 at 11:09, Nikhil Maroli  wrote:

> Hello ,
>
> can anyone tell me why im getting profile like this after umbrella
> simulation
>
> im attaching both hist.xvg and profile.xvg plot
>
> histo plot
>
>
> https://drive.google.com/file/d/0BxaQk_pcR9viaGRNQlhrcVVmazQ/view?usp=sharing
>
> profile
>
>
> https://drive.google.com/file/d/0BxaQk_pcR9viMHNOTE5Ba3VlY2c/view?usp=sharing
>
> Thanks
> Nikhil
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[gmx-users] umbrella simulation PMF curve

[Nikhil Maroli]

Hello ,

can anyone tell me why im getting profile like this after umbrella
simulation

im attaching both hist.xvg and profile.xvg plot

histo plot

https://drive.google.com/file/d/0BxaQk_pcR9viaGRNQlhrcVVmazQ/view?usp=sharing

profile

https://drive.google.com/file/d/0BxaQk_pcR9viMHNOTE5Ba3VlY2c/view?usp=sharing

Thanks
Nikhil
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Re: [gmx-users] fix COM

[Ming Tang]

Thank you Mark,

Could you please help to give more instructions on how to generate restraints 
on a centre of mass virtual site? I know genrestr can implement restraints, but 
I have no idea how to set a virtual site.

BTW:  is the latest version suitable for mpt 2.13?  it seems that version 5.0.4 
does not work.

Thanks,
Ming
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Re: [gmx-users] fix COM

[Ming Tang]

Hi Justin,

Thanks for your information. My atom group contains only 3 atoms, each of which 
is on one chain of a triple helix. Flat-bottomed is new for me. I went through 
section 4.3.2 in the manual, but still feel confused about how to get the 
parameters and how to apply constraints. Do you think flat-bottomed is suitable 
for my case?

Thank you,
Ming
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Re: [gmx-users] fix COM

[Mark Abraham]

Or probably on a centre of mass virtual site.

Mark

On Sun, 21 Feb 2016 21:27 Justin Lemkul  wrote:

>
>
> On 2/20/16 10:44 PM, Ming Tang wrote:
> > Dear Gromacs experts,
> >
> > Is there a approach to fix the centre of mass of a group of atoms only
> without fixing all of the atoms during a stretching process?
> >
>
> No, but you can approximate such behavior using a flat-bottom position
> restraint
> on judiciously chosen atoms.
>
> -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] Potential energy

[mohammad r]

Thank you Justin,
do you know how I can find or modify the center of mass velocity of my system? 

On Sunday, February 21, 2016 11:50 PM, Justin Lemkul  
wrote:
 

 

On 2/21/16 3:15 PM, mohammad r wrote:
> Hi everybody,
>
>
>
> Is it correct to say the potential energy after energyminimization should be 
> negative and in the order of 105-106 ?according to gromacs tutorial:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
>

As a broad generalization, but strictly speaking, that's not always true.  A 
comparable protein in a similarly sized box will probably have something on 
that 
order, but that is by no means an absolute rule.

-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
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Re: [gmx-users] fix COM

[Justin Lemkul]

On 2/20/16 10:44 PM, Ming Tang wrote:

Dear Gromacs experts,

Is there a approach to fix the centre of mass of a group of atoms only without 
fixing all of the atoms during a stretching process?



No, but you can approximate such behavior using a flat-bottom position restraint 
on judiciously chosen atoms.


-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] position restraints for different protein atoms

[Justin Lemkul]

On 2/20/16 11:16 PM, Irem Altan wrote:

Hi,

Is there a way to generate position restraint files such that the main chain
atoms and the side chain atoms have different force constants? Similarly,


Yes, you can invoke genrestr with a suitable index group for whatever part of 
the protein you want to set up with a given force constant.



would it be possible to constrain atoms with B-factors lower than a certain
threshold?



Only if you devise a way to parse such information.  That probably involves 
writing your own script to parse the B-factors in a PDB file and write those 
atom numbers to an index file, which can then be fed to genrestr as stated above.


-Justin

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==

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
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Re: [gmx-users] docking

[Justin Lemkul]

On 2/21/16 4:14 AM, Negar Parvizi wrote:

Thank you so much for your help.
Should  I use protein-ligand complex tutorial for MD simulation of docked 
complexes?



Unless the "ligand" is a polypeptide or some other biological molecule that is 
described in the force field, yes, that's pretty much the exact case for which 
the tutorial is designed.


-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
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Re: [gmx-users] Embedding Protein into lipid bilayer

[Justin Lemkul]

On 2/21/16 5:44 AM, khourshaeisha...@mech.sharif.ir wrote:




p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }


Dear Justin


first of all, thanks for your replay. but I should cite that the bizarre
character that you saw in my Email was Sharif university Email domains
fault not me. also different copies of Email was because of the fact that
I didnt know how to use gmx-user. from now on, I try not to bother my
friends in gmx-user anymore.


to be honest, I need to simulate a cell membrane with 1r2c protein and
exert some tests like creep and compliance onto it to obtain viscoelastic
response of it. after finishing your tutorial, I thought that now I can
do it. I downloaded 1r2c pretin from PDB bank. but unfortunately at the
beginning I confront with fatal error. I really appreciate it if you
answer my below question.


1. the PDB which we usually download from PDB bank is Full length not a
peptide.isnt it?



Depends on the protein.



2. Can I use the full length PDB file or I should change it to obtain a
peptide?



Simulate whatever is relevant to your scientific question(s) at hand.  You do 
not need to conform to some simple tutorial example.  Tutorials are, by design, 
some small and reproducible system.  "Real" science is often much more complex.




3. about the desired output I explained above, Can I obtain it based on
the method you used in tutorial?



I don't really know what any of that is.  Use literature as your guide.  The 
tutorial is a simple how-to for setting up a heterogeneous system.  How you 
carry out and analyze the subsequent simulation depends entirely upon what you 
want to observe.




4. If I use gmx pdb2gmx -f 1rc2.pdb -o 1rc2_processed.gro -ignh�
-water spc, I mean without -ter, It says:


Fatal error:

There were 35 missing atoms in molecule Protein_chain_B, if you want to
use this incomplete topology anyhow, use the option -missing


can I keep on using -missing or not?



Absolutely not.  This will build an incomplete model that is physically 
unrealistic.  As a general rule, NEVER use -missing.  It is for niche cases 
only.  Check your input PDB structure for obvious MISSING entries that tell you 
about parts of the structure that were not resolved.  If these are internal 
residues, you need to build them using the appropriate modeling software (not 
GROMACS).


-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
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Re: [gmx-users] umbrella simulation -pulling in other directions

[Justin Lemkul]

On 2/21/16 8:28 AM, Nikhil Maroli wrote:

Dear all,
i am doing Umbrella sampling,as my ligand is in x axis after i made a
box,so i have to pull it towards -x direction instead of z which mention in
tutorial, can i give
pull_coord1_rate= -0.01
negative rate? is it make any sense or is there any ohter method to pull in
-X direction
i have attached an  image,waiting for the valuable suggestions!!



A negative pull rate causes the COM distance between the pulled and reference 
groups to decrease over time.  It does not necessarily dictate the direction 
along an axis in which the pulled group will move.  To pull along -x you need to 
set pull-coord1-vec appropriately.


-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
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Re: [gmx-users] Potential energy

[Justin Lemkul]

On 2/21/16 3:15 PM, mohammad r wrote:

Hi everybody,



Is it correct to say the potential energy after energyminimization should be 
negative and in the order of 105-106 ?according to gromacs tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html



As a broad generalization, but strictly speaking, that's not always true.  A 
comparable protein in a similarly sized box will probably have something on that 
order, but that is by no means an absolute rule.


-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] Potential energy

[mohammad r]

Hi everybody,


 
Is it correct to say the potential energy after energyminimization should be 
negative and in the order of 105-106 ?according to gromacs tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html


Thank you, Mohammad.
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Re: [gmx-users] converted topology from amber to gromacs

[mohammad r]

Thank you very much Justin 

On Saturday, February 20, 2016 10:53 PM, Justin Lemkul  
wrote:
 

 

On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file of my systems. Can you please take a look at this and
> tell me your opinion? You mean that it doesn't make any problem when after
> conversion process the topology file doesn't refer to any force field?
>

The topology lists all needed parameters explicitly.  Note the header that says 
"This is a standalone topology."  "Standalone" means "I have everything you 
need 
right here."

The purpose of the #include function in GROMACS is to say "copy and paste the 
contents of the file here."  That is the same thing for grompp as listing all 
parameters explicitly.

There is no problem here with your topology.  It just looks a little different, 
but if you understand a little bit about how GROMACS assembles topologies, it 
becomes obvious that this is a slightly more verbose version of what you are 
used to seeing.

-Justin

> Thank you, Mohammad.
>
>
>
>
> On Friday, February 19, 2016 4:38 PM, Justin Lemkul  wrote:
>
>
>
>
> On 2/19/16 3:26 AM, mohammad r wrote:
>  >
>  > I don't know whether the problem is with the converting process (gromacs
> topology file doesn't refer to any force filed) or the the process of 
> generating
> files in amber tools is wrong.
>  >
>
> Are you getting some specific problem in GROMACS?  ParmEd should give you a
> self-contained topology file that explicitly lists the parameters it uses.  It
> may not fit the convention of the normal sequence of #include statements 
> because
> it's using a slightly different, but equally valid, approach.
>
> Without seeing your topology, it's impossible to figure out if there is any
> problem.  grompp is the quickest test here.  If it doesn't complain, you're 
> fine.
>
> -Justin
>
>  >      On Friday, February 19, 2016 11:04 AM, mohammad r
> > wrote:
>  >
>  >
>  >  #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}I used
> ff14SBAmber protein force field, #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}
> LIPID11force field and TIP3P water model. First I  loaded the force fields and
> water model then loaded the pdb file and finally I saved the topology and
> coordinate files.
>
>  >
>  >
>  >      On Friday, February 19, 2016 10:40 AM, Hai Nguyen  > wrote:
>  >
>  >
>  >  Hi
>  > You should know which AMBER force field when you made the topology file. 
>(How
> did you make it?)
>  > Hai
>  > On Fri, Feb 19, 2016 at 12:56 AM, mohammad r  > wrote:
>  >
>  > Hi gromacs users,
>  > I've generatedinitial structure of my system by using ambertools (topology
> andcoordinate files) and converted it to gromacs format (.gro and .top)by
> parmed, but in topology file it doesn't refer to any forcefield.Does it make 
> any
> problem in the results or it is ok? Because when Icompare the simulation 
> result
> with experiment it is incorrect.
>  > Thank you, Mohammad.
>  > --
>  > Gromacs Users mailing list
>  >
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before posting!
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> or send a
> mail to gmx-users-requ...@gromacs.org. 
>
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>
> --
> ==
>
> 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
>
>
> ==
>
>

-- 
==

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 

[gmx-users] Screenshot from 2016-02-21 18:45:00.png

[Nikhil M (via Google Drive)]

I've shared an item with you:

Screenshot from 2016-02-21 18:45:00.png
https://drive.google.com/file/d/0BxaQk_pcR9viTURiNWVJR3NfS3M/view?usp=sharing=CLDlkagE=56c9bb79

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[gmx-users] umbrella simulation -pulling in other directions

[Nikhil Maroli]

Dear all,
i am doing Umbrella sampling,as my ligand is in x axis after i made a
box,so i have to pull it towards -x direction instead of z which mention in
tutorial, can i give
pull_coord1_rate= -0.01
negative rate? is it make any sense or is there any ohter method to pull in
-X direction
i have attached an  image,waiting for the valuable suggestions!!


https://drive.google.com/file/d/0BxaQk_pcR9viTURiNWVJR3NfS3M/view?usp=sharing


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Ragards,
Nikhil Maroli
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[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }


Dear Justin


first of all, thanks for your replay. but I should cite that the bizarre
character that you saw in my Email was Sharif university Email domains
fault not me. also different copies of Email was because of the fact that
I didnt know how to use gmx-user. from now on, I try not to bother my
friends in gmx-user anymore.


to be honest, I need to simulate a cell membrane with 1r2c protein and
exert some tests like creep and compliance onto it to obtain viscoelastic
response of it. after finishing your tutorial, I thought that now I can
do it. I downloaded 1r2c pretin from PDB bank. but unfortunately at the
beginning I confront with fatal error. I really appreciate it if you
answer my below question.


1. the PDB which we usually download from PDB bank is Full length not a
peptide.isnt it?


2. Can I use the full length PDB file or I should change it to obtain a
peptide?


3. about the desired output I explained above, Can I obtain it based on
the method you used in tutorial?


4. If I use gmx pdb2gmx -f 1rc2.pdb -o 1rc2_processed.gro -ignh�
-water spc, I mean without -ter, It says:


Fatal error:

There were 35 missing atoms in molecule Protein_chain_B, if you want to
use this incomplete topology anyhow, use the option -missing


can I keep on using -missing or not?


Finally, I should again thank you because of your helps.


best regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran

The tutorial uses a modeled peptide fragment.  Typically fragments of larger
proteins are capped with neutral groups to avoid artifacts of charged termini
that normally wouldnt be there, or to match some experimental data that used
the same form (as is actually the case here).

Dont choose "None" for termini unless you have constructed such
groups.  It
makes no physical or biological sense.  If you have a full-length protein,
these
will have normal termini.  Refer to any basic biochemistry text if you are
unfamiliar with what peptide bonds or protein termini are.

-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




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