subject:"\[gmx\-users\] Re\: GPCR MD Tutorial Using GROMACS $URL$"

Dear Justin

Thanks for the explanation.

I am following your tutorial of KALP membrane simulation. I am stuck in
between two steps of InflateGRO. After the first step, the tutorial requests
to perform EM. Should I be running grompp with new system_inflated.gro file
to generate a new .tpr file for EM or should I perform EM with em.tpr which
was generated some time back in the tutorial? The latter ran EM but the
former shows error 'number of coordinates in coordinate file
(system_inflated.gro, 6438)
 does not match topology (topol.top, 17403)

Thanks.

Bala S


--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 1:01 PM, Bala S think_bey...@aol.com wrote:

Dear Justin

Thanks for the explanation.

I am following your tutorial of KALP membrane simulation. I am stuck in
between two steps of InflateGRO. After the first step, the tutorial
requests
to perform EM. Should I be running grompp with new system_inflated.gro file
to generate a new .tpr file for EM or should I perform EM with em.tpr
which

was generated some time back in the tutorial?

You should run grompp with the inflated .gro file (system_inflated.gro)
since you will be minimizing the inflated .gro file after every compression
step to remove bad contacts. The earlier em.tpr was used to remove
periodicity of the bilayer only.

The latter ran EM but the
former shows error 'number of coordinates in coordinate file
(system_inflated.gro, 6438)
does not match topology (topol.top, 17403)

The difference in atom numbers might be because your .top file contains
some extra molecules in the [ molecules ] section (may be SOL). Use .top
file that contains only protein and lipid molecules.

Thanks.

Bala S

--
View this message in context:
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

Thank you for that clarification.

I found that there were SOL molecules in .top file. I could run the EM now.

Coming to the Solvation step, I'm facing a problem.

I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
locally. 

While adding the solvent molecules, what command should I be using?

I am using the usual command I use for non-membrane simulations,

$ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic

followed by 

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

calculation goes for long time showing a huge number of SOL molecules.

I guess I'm worng somehere.

Thanks.

Bala S





--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 3:27 PM, Bala S think_bey...@aol.com wrote:

Thank you for that clarification.

I found that there were SOL molecules in .top file. I could run the EM now.

Coming to the Solvation step, I'm facing a problem.

I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
locally.

While adding the solvent molecules, what command should I be using?

I am using the usual command I use for non-membrane simulations,

$ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic

followed by

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

When you mention -bt cubic, it adds a cubic water box all around your
system (if you visualize you will see your entire bilayer immersed in a
cubic water box like a normal protein solvation). But that is wrong. You
need to add water only on either side of the lipid membrane (that is along
the z-axis only). So use the -box option with editconf without using -c and
-d. You can have a look at
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly
mentioned over there how to go about it.

calculation goes for long time showing a huge number of SOL molecules.

I guess I'm worng somehere.

Thanks.

Bala S

--
View this message in context:
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On 4/27/12 6:04 AM, Anirban Ghosh wrote:

On Fri, Apr 27, 2012 at 3:27 PM, Bala S think_bey...@aol.com
mailto:think_bey...@aol.com wrote:

Thank you for that clarification.

I found that there were SOL molecules in .top file. I could run the EM now.

Coming to the Solvation step, I'm facing a problem.

I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
locally.

While adding the solvent molecules, what command should I be using?

I am using the usual command I use for non-membrane simulations,

$ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic

followed by

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

When you mention -bt cubic, it adds a cubic water box all around your system (if
you visualize you will see your entire bilayer immersed in a cubic water box
like a normal protein solvation). But that is wrong. You need to add water only
on either side of the lipid membrane (that is along the z-axis only). So use the
-box option with editconf without using -c and -d. You can have a look at
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly
mentioned over there how to go about it.

You should not add water in between InflateGRO steps. The process should be
carried out entirely in the absence of water, otherwise you add solvent to a
huge box and the water is incorporated into the voids in the lipid membrane.
Only after the last shrinking step should you proceed with adding water.

-Justin

calculation goes for long time showing a huge number of SOL molecules.

I guess I'm worng somehere.

Thanks.

Bala S

--
View this message in context:

http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Thanks for the reply.

I'm following the tutorial.

In your system, to solvate it you have the values that was used during the
protien insertion into the bilayer. Following it, I have used the following
commandfor my system where the protein is very much smaller than the length
of the bilayer.

$ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

But I could see in the visualizer that SOL molecules were added on top and
bottom but only 1/3 of the length of the bilayer. 
How to add SOL molecules to whole length or how to remove not-solvated part
of lipids?

Thanks
Bala S

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933536.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)




On 4/27/12 6:40 AM, Bala S wrote:

Thanks for the reply.

I'm following the tutorial.



Please clarify whether you're using Anirban's or mine.  Now that two exist, 
people will have to be a fair bit more specific :)



In your system, to solvate it you have the values that was used during the
protien insertion into the bilayer. Following it, I have used the following
commandfor my system where the protein is very much smaller than the length
of the bilayer.

$ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top



If you have to manipulate the box of any coordinate file produced by InflateGRO, 
whatever you're doing is wrong.  You should not be solvating anything until the 
very last step of the procedure, where your bilayer is of correct size and APL.



But I could see in the visualizer that SOL molecules were added on top and
bottom but only 1/3 of the length of the bilayer.
How to add SOL molecules to whole length or how to remove not-solvated part
of lipids?



This outcome is a consequence of re-adjusting the box size of a system that 
likely has other dimensions.  As far as I can tell, you shouldn't be doing this.


-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


--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul jalem...@vt.edu wrote:

On 4/27/12 6:40 AM, Bala S wrote:

Thanks for the reply.

I'm following the tutorial.

Please clarify whether you're using Anirban's or mine. Now that two
exist, people will have to be a fair bit more specific :)

In your system, to solvate it you have the values that was used during the
protien insertion into the bilayer. Following it, I have used the
following
commandfor my system where the protein is very much smaller than the
length
of the bilayer.

$ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350
6.59650

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

If you have to manipulate the box of any coordinate file produced by
InflateGRO, whatever you're doing is wrong. You should not be solvating
anything until the very last step of the procedure, where your bilayer is
of correct size and APL.

Exactly, solvate at the end of all the compression steps performed by
InflateGro (may be 10 or 20 depending on your system) and minimizations (of
only protein + lipid) until you have reached the correct area per lipid.
And then only solvate. Check for the dimensions in the last line of the
FINAL (compressed and minimized) .gro file and then solvate

Thanks,

Anirban

But I could see in the visualizer that SOL molecules were added on top and
bottom but only 1/3 of the length of the bilayer.
How to add SOL molecules to whole length or how to remove not-solvated
part
of lipids?

This outcome is a consequence of re-adjusting the box size of a system
that likely has other dimensions. As far as I can tell, you shouldn't be
doing this.

-Justin

--
==**==

==**==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Thanks Justin and Anirban for taking this long in TM simulations.

I'm following Justin's tutorial majorly and taking some clues from Anirban's
too when I need further clarification.

From both of your guidelines I could understand wht I should be doing before
solvating the system. Now, I have a question that how many iterations I
should perform with inflateGRO program and what is the basis to stop and
move with solvation step?

Justin's one says that he could reach ~72 Å2 (which is above the expt. value
~62Å2). But when I am exactly following the tutorial with same KALP peptide.
I am ending up with 'Area per lipid: 3.73355898918962 nm^2' within 10
iterations which is far lower than Justin's. Why?

Thanks.

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933801.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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] Re: GPCR MD Tutorial Using GROMACS (URL)




On 4/27/12 8:38 AM, Bala S wrote:

Thanks Justin and Anirban for taking this long in TM simulations.

I'm following Justin's tutorial majorly and taking some clues from Anirban's
too when I need further clarification.


From both of your guidelines I could understand wht I should be doing before

solvating the system. Now, I have a question that how many iterations I
should perform with inflateGRO program and what is the basis to stop and
move with solvation step?

Justin's one says that he could reach ~72 Å2 (which is above the expt. value
~62Å2). But when I am exactly following the tutorial with same KALP peptide.
I am ending up with 'Area per lipid: 3.73355898918962 nm^2' within 10
iterations which is far lower than Justin's. Why?



3.73 nm^2 is 373 A^2 - mind the fact that the units have a square term.

-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


--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

Justin,

OOPS!!
Sorry for that.. Now I could realize it.
Following up.. I have done further iterations with inflategro and reached
0.62 nm^2 which similar to what you have explained in the tutorial.

Now, I could see the lipid bilayer really shrinked and no SOL molecules are
seen in between. Now the issue I would like to have clarification on is that
only 163 SOL molecules were added up and down which looks very scarce for
the simulation.

What is the solution?

Bala S

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 6:31 PM, Bala S think_bey...@aol.com wrote:

Justin,

OOPS!!
Sorry for that.. Now I could realize it.
Following up.. I have done further iterations with inflategro and reached
0.62 nm^2 which similar to what you have explained in the tutorial.

Now, I could see the lipid bilayer really shrinked and no SOL molecules are
seen in between. Now the issue I would like to have clarification on is
that
only 163 SOL molecules were added up and down which looks very scarce for
the simulation.

What is the solution?

First visualize and see whether the hydrophilic ends of the lipid bilayer
and your protein's part on either side of the bilayer (like a GPCR's intra
and extra cellular ends) are well immersed in the water box. If not, you
can increase the solvation box along the z-axis by increasing the z value
for -box option in editconf (keeping x and y values same).

Anirban

Bala S

--
View this message in context:
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

Anirban,

Thank you. You guys are doing miracles with the biomolecules and solving
almost all of my problems.

I have followed your suggestion and could see now some more SOL molecules by
increasing the z value.

But I am seeing a substantial gap between the surface of the lipid bilayer
and added SOL molecules in the visualizer. Is it normal or I have to do
something about it?

Thanks
Bala S

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 7:00 PM, Bala S think_bey...@aol.com wrote:

Anirban,

Thank you. You guys are doing miracles with the biomolecules and solving
almost all of my problems.

I have followed your suggestion and could see now some more SOL molecules
by
increasing the z value.

But I am seeing a substantial gap between the surface of the lipid bilayer
and added SOL molecules in the visualizer. Is it normal or I have to do
something about it?

I didn't really get your point. From the surface means on either side of
the leaflets? Or one thing you can do is to carry out the EM, and
equilibration runs (NVT and NPT) (restraining the protein) and see how the
waters orient them with respect to the bilayer.

Anirban

Thanks
Bala S

--
View this message in context:
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

Anirban,

Exactly.. That's the gap (either side of the leaflets) I was mentioning
about. I'll try EM and check itagain.

Thanks.

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933996.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)




On 4/27/12 10:00 AM, Bala S wrote:

Anirban,

Exactly.. That's the gap (either side of the leaflets) I was mentioning
about. I'll try EM and check itagain.



EM won't fill in solvent gaps.  If you're using my protocol for increasing the C 
radius in vdwradii.dat, then a small gap is normal and will close when doing 
equilibration as the solvent fills in around the lipid headgroups.


-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


--
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] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 On 4/27/12 10:00 AM, Bala S wrote:

 Anirban,

 Exactly.. That's the gap (either side of the leaflets) I was mentioning
 about. I'll try EM and check itagain.


 EM won't fill in solvent gaps.  If you're using my protocol for increasing
 the C radius in vdwradii.dat, then a small gap is normal and will close
 when doing equilibration as the solvent fills in around the lipid
 headgroups.

  Yes, as Justin mentioned, the equilibration runs (restraining the
protein) will fill those gaps.

Anirban

-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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists

-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)

Hi Justin and Anirban,

I've seen that most of the SOL molecules movin towards the head groups after
NVT equilibrium run as mentioned in Justin's. I'm wiating for my NPT run to
complete. Hopefully I can see all of them aliging over the headgroups.

Thanks


--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4934356.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] Re: GPCR MD Tutorial Using GROMACS (URL)