Re: [gmx-users] About Packaging of Protein by Lipids

[Justin Lemkul]

On 10/25/12 11:40 AM, vidhya sankar wrote:

Dear Justin Thank you for your Previous reply,

 But When I use Vandewalls Radii for Carbon Atom 0.375 As Quoted in your 
tutorial  Then My Protein-Lipid System is solvated with 22000 Water Molecules  
Most of them are Within  Bilayer .  This is Huge number  I Think

From  your reply Mail I came  to Conclusion  that I need to  Pack Lipid 
effectively Around Protein using
inflategro .pl script   (By doing More number of iterations Than I did Before  
)  Thereby I can Eliminate  Presence of Void In my system

Is My  Above Understanding   is correct or Not ?



Yes.


Also When I do the more Iteration using  inflategro.pl  script

My  area per lipid Is very less than Experimental value for DPPC lipid (62 A)



InflateGRO overestimates the APL value, so your DPPC are probably very 
over-compressed at this point.



Then  Can  i continue My solvationwith this  Low area ( I am using Box size 
of 6 6 6 )



I'm not going to try to blindly judge whether or not that will work.  You know 
what you need to do.  Try it and see.


-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/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

[gmx-users] About Packaging of Protein by Lipids

[vidhya sankar]

Dear Justin Thank you for your Previous reply,
    
But When I use Vandewalls Radii for Carbon Atom 0.375 As Quoted in your 
tutorial  Then My Protein-Lipid System is solvated with 22000 Water Molecules  
Most of them are Within  Bilayer .  This is Huge number  I Think

From  your reply Mail I came  to Conclusion  that I need to  Pack Lipid 
effectively Around Protein using
inflategro .pl script   (By doing More number of iterations Than I did Before  
)  Thereby I can Eliminate  Presence of Void In my system  

Is My  Above Understanding   is correct or Not ?

Also When I do the more Iteration using  inflategro.pl  script 

My  area per lipid Is very less than Experimental value for DPPC lipid (62 A)  

Then  Can  i continue My solvation    with this  Low area ( I am using Box size 
of 6 6 6 )

Thanks In Advance
--
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

Re: [gmx-users] Freeze group atoms changing position

[Bogdan Costescu]

On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall  wrote:
> Thanks Justin. I identified the offending waters using vmd (adding 1 to
> resID and atom number since vmd starts counting at 0) and checked
> confout.gro to make sure the coordinates matched up. I only have one group
> for all frozen atoms in the system, and these guys are definitely in it.

Are you using some kind of constraints ? Are you using energy group
exclusions to avoid interactions between frozen atoms ? If you search
the manual for "frozen" you'll find some warnings and recommendations.

Cheers,
Bogdan
-- 
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

Re: [gmx-users] Freeze group atoms changing position

[Justin Lemkul]

On 10/25/12 9:59 AM, Alex Marshall wrote:

Thanks Justin. I identified the offending waters using vmd (adding 1 to
resID and atom number since vmd starts counting at 0) and checked
confout.gro to make sure the coordinates matched up. I only have one group
for all frozen atoms in the system, and these guys are definitely in it.



Then I'm stumped.  Freezing shouldn't partially work - either it does or 
doesn't, and I've never seen anything like this.  As a test, do simple position 
restraints fare better?


-Justin


On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul  wrote:




On 10/24/12 3:17 PM, Alex Marshall wrote:


Hi all,

I'm simulating a system of two reservoirs connected by a carbon nanotube.
The reservoir wall atoms and carbon nanotube atoms are held in place using
freeze groups at all times. I'm currently equilibrating the reservoirs
separately by also freezing the water inside the nanotube, but after 20 ns
two of the frozen water molecules have jumped outside of the nanotube into
a supposedly inaccessible region. What could cause this? Should I be
worried?



I would be.  Frozen groups aren't supposed to move at all.  Verify that
the problematic water molecules are indeed contained within whatever frozen
group(s) you have assigned in the .mdp file.  Otherwise, there's no
immediate explanation, especially since other frozen atoms are staying
frozen.

-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!
* 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







--


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/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

Re: [gmx-users] About Diffusion of Solvent Molecules

[Justin Lemkul]

On 10/25/12 10:16 AM, vidhya sankar wrote:

Dear Justin,

   Thank you for your Previous reply.
I am Extending your Protein Lipid tutorial To my System I am using DPPC128.pdb  
Which Surround the Cyclic Peptide. As You Quoted in tutorial I am Solvating My 
Lipid-protein Environment Using 148 Molecules (By genbox tools while

I am using  Vanderwalls Radii 0.92 for Carbon atom )   When I visualize .gro 
File in VMD Most of the water Molecules Are near the  Face of My box ( Away 
from center)   while Lipid  molecules are concentrated Around Protein Which is 
at  The center of box .



You should never use such a radius for carbon.  You will have huge voids in your 
system that will become unstable.  If a smaller value of carbon radius (on the 
order of 0.375 nm) is still putting water molecules in bad locations (i.e. 
within the bilayer), then your lipids are not sufficiently packed or 
equilibrated.  If you find yourself using extreme measures just to construct the 
system, it's probably wrong.



After  Second Phase Equilibration (After NPT ,Same Parameter ) When  I see .gro 
file in VMD   Most of Water Molecules moved  inside the box  ( Surround the  
Protein  along with  the Lipid molecules )
Is this Type of Diffusion of Solvent molecules is Usual or Not.


I don't have a clear picture of what you're describing, but it certainly sounds 
wrong if my imagination is correct.



What  I mean

Should it (Water Molcules)  Be Nearer to face of the Box Throughout  Entire MD 
. or Need not be like That?



You should have layers of solvent on either face of the membrane-protein 
complex.  The box should be filled (with no voids) and there should be no 
obvious asymmetry.


-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/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

[gmx-users] About Diffusion of Solvent Molecules

[vidhya sankar]

Dear Justin, 

  Thank you for your Previous reply.
I am Extending your Protein Lipid tutorial To my System I am using DPPC128.pdb  
Which Surround the Cyclic Peptide. As You Quoted in tutorial I am Solvating My 
Lipid-protein Environment Using 148 Molecules (By genbox tools while   

I am using  Vanderwalls Radii 0.92 for Carbon atom )   When I visualize .gro 
File in VMD Most of the water Molecules Are near the  Face of My box ( Away 
from center)   while Lipid  molecules are concentrated Around Protein Which is 
at  The center of box . 

After  Second Phase Equilibration (After NPT ,Same Parameter ) When  I see .gro 
file in VMD   Most of Water Molecules moved  inside the box  ( Surround the  
Protein  along with  the Lipid molecules )
Is this Type of Diffusion of Solvent molecules is Usual or Not.
What  I mean  

Should it (Water Molcules)  Be Nearer to face of the Box Throughout  Entire MD 
. or Need not be like That? 

Thanks In Advance
--
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

Re: [gmx-users] Freeze group atoms changing position

[Alex Marshall]

Thanks Justin. I identified the offending waters using vmd (adding 1 to
resID and atom number since vmd starts counting at 0) and checked
confout.gro to make sure the coordinates matched up. I only have one group
for all frozen atoms in the system, and these guys are definitely in it.

On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul  wrote:

>
>
> On 10/24/12 3:17 PM, Alex Marshall wrote:
>
>> Hi all,
>>
>> I'm simulating a system of two reservoirs connected by a carbon nanotube.
>> The reservoir wall atoms and carbon nanotube atoms are held in place using
>> freeze groups at all times. I'm currently equilibrating the reservoirs
>> separately by also freezing the water inside the nanotube, but after 20 ns
>> two of the frozen water molecules have jumped outside of the nanotube into
>> a supposedly inaccessible region. What could cause this? Should I be
>> worried?
>>
>>
> I would be.  Frozen groups aren't supposed to move at all.  Verify that
> the problematic water molecules are indeed contained within whatever frozen
> group(s) you have assigned in the .mdp file.  Otherwise, there's no
> immediate explanation, especially since other frozen atoms are staying
> frozen.
>
> -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!
> * 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
>



-- 
Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario
-- 
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

Re: [gmx-users] some warnings

[Albert]

On 10/25/2012 03:07 PM, Justin Lemkul wrote:
Notes and warnings are different.  In this case, grompp is advising 
you that some of your settings are inappropriate.  For note 1, do what 
it says.  If you don't know why, Google "flying ice cube effect." For 
notes 2 and 3, it is simply telling you that your settings are wrong 
and it is fixing them.


-Justin


thank you very much
Albert
--
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

Re: [gmx-users] some warnings

[Justin Lemkul]

On 10/25/12 8:52 AM, Albert wrote:

hello:

  I am using GBSA solvent for replica exchange simulation. However, I've got
three wanrnigns when I generate .tpr file:


NOTE 1 [file eq_11.mdp]:
   Tumbling and or flying ice-cubes: We are not removing rotation around
   center of mass in a non-periodic system. You should probably set
   comm_mode = ANGULAR.


NOTE 2 [file eq_11.mdp]:
   Using GBSA with nstgbradii<1, setting nstgbradii=1


NOTE 3 [file eq_11.mdp]:
   Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936
   kJ/nm^2/mol for Still and HCT/OBC respectively




Notes and warnings are different.  In this case, grompp is advising you that 
some of your settings are inappropriate.  For note 1, do what it says.  If you 
don't know why, Google "flying ice cube effect."  For notes 2 and 3, it is 
simply telling you that your settings are wrong and it is fixing them.


-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/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

[gmx-users] some warnings

[Albert]

hello:

 I am using GBSA solvent for replica exchange simulation. However, I've 
got three wanrnigns when I generate .tpr file:



NOTE 1 [file eq_11.mdp]:
  Tumbling and or flying ice-cubes: We are not removing rotation around
  center of mass in a non-periodic system. You should probably set
  comm_mode = ANGULAR.


NOTE 2 [file eq_11.mdp]:
  Using GBSA with nstgbradii<1, setting nstgbradii=1


NOTE 3 [file eq_11.mdp]:
  Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936
  kJ/nm^2/mol for Still and HCT/OBC respectively


thank you very much
Albert
--
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

Re: [gmx-users] Can't center box with trjconv

[Erik Marklund]

Try e.g. trjconv -pbc mol -trans ? ? ? to have your molecule not span the edges 
first. You might also need a trjconv -pbc nojump and trjconv -pbc -mol again 
afterwards before centering.
 
25 okt 2012 kl. 13.44 skrev Ignacio Fernández Galván:

> I must be doing something wrong, but I can't get trjconv to center the 
> simulation on a residue.
> 
> The simulation box is cubic, the system is formed by an 8-atom frozen 
> molecule and 800 water molecules. I try to center the box with:
> 
>  $ trjconv -f system.cpt -s system.tpr -o conf.gro -center
> 
> (system.cpt and system.tpr are the result of a simulation)
> 
> I select group "2" (the frozen molecule) as a center group, and I get this in 
> the output conf.gro:
> 
>1ACR C11   0.074   0.042   1.443  0.  0.  0.
>1ACR H12   0.130   0.139   1.443  0.  0.  0.
>1ACR  O3   0.133   2.822   1.443  0.  0.  0.
>1ACR C24   2.811   0.056   1.443  0.  0.  0.
>1ACR H25   2.771   0.158   1.443  0.  0.  0.
>1ACR C36   2.731   2.834   1.443  0.  0.  0.
>1ACRH3a7   2.622   2.843   1.443  0.  0.  0.
>1ACRH3b8   2.775   2.734   1.443  0.  0.  0.
> 
> as you see, the molecule is clearly broken (a difference of more than 2 nm in 
> coordinates), and when visualized, it's indeed in the box's edge.
> 
> I've tried with different combinations of -pdb res/mol, -boxcenter 
> zero/tric/rect, -ur compact, but I always get the molecule broken, sometimes 
> in a corner, sometimes in an edge.
> 
> In case it matters, the initial configuration for the simulation has:
> 
>1ACR C11   0.138870   0.039109   0.00
>1ACR H12   0.195321   0.135855   0.00
>1ACR  O3   0.197788  -0.067044   0.00
>1ACR C24  -0.009210   0.052984   0.00
>1ACR H25  -0.049761   0.154673   0.00
>1ACR C36  -0.089322  -0.054436   0.00
>1ACRH3a7  -0.198186  -0.045502   0.00
>1ACRH3b8  -0.045500  -0.154639   0.00
> 
> and, as I said, this residue (and molecule) is set as frozen, and it is 
> actually frozen during the simulation.
> 
> Is there some bug/limitation in trjconv? Am I doing something wrong?
> 
> Thanks,
> Ignacio
> --
> 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

---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

--
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

[gmx-users] Can't center box with trjconv

[Ignacio Fernández Galván]

I must be doing something wrong, but I can't get trjconv to center the 
simulation on a residue.

The simulation box is cubic, the system is formed by an 8-atom frozen molecule 
and 800 water molecules. I try to center the box with:

  $ trjconv -f system.cpt -s system.tpr -o conf.gro -center

(system.cpt and system.tpr are the result of a simulation)

I select group "2" (the frozen molecule) as a center group, and I get this in 
the output conf.gro:

1ACR C11   0.074   0.042   1.443  0.  0.  0.
1ACR H12   0.130   0.139   1.443  0.  0.  0.
1ACR  O3   0.133   2.822   1.443  0.  0.  0.
1ACR C24   2.811   0.056   1.443  0.  0.  0.
1ACR H25   2.771   0.158   1.443  0.  0.  0.
1ACR C36   2.731   2.834   1.443  0.  0.  0.
1ACRH3a7   2.622   2.843   1.443  0.  0.  0.
1ACRH3b8   2.775   2.734   1.443  0.  0.  0.

as you see, the molecule is clearly broken (a difference of more than 2 nm in 
coordinates), and when visualized, it's indeed in the box's edge.

I've tried with different combinations of -pdb res/mol, -boxcenter 
zero/tric/rect, -ur compact, but I always get the molecule broken, sometimes in 
a corner, sometimes in an edge.

In case it matters, the initial configuration for the simulation has:

1ACR C11   0.138870   0.039109   0.00
1ACR H12   0.195321   0.135855   0.00
1ACR  O3   0.197788  -0.067044   0.00
1ACR C24  -0.009210   0.052984   0.00
1ACR H25  -0.049761   0.154673   0.00
1ACR C36  -0.089322  -0.054436   0.00
1ACRH3a7  -0.198186  -0.045502   0.00
1ACRH3b8  -0.045500  -0.154639   0.00

and, as I said, this residue (and molecule) is set as frozen, and it is 
actually frozen during the simulation.

Is there some bug/limitation in trjconv? Am I doing something wrong?

Thanks,
Ignacio
--
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