Re: [gmx-users] semi-permeable wall in gromacs

[Justin Lemkul]

On 4/19/16 9:06 AM, gozde ergin wrote:

Is refcoord_scaling the issue for also NVT simulation?


No, it only applies when pressure coupling is applied.


Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.



The information you've provided (based on file names and .mdp files) suggests 
you've done this backwards; your data collection should be in NVT so the problem 
I mentioned shouldn't matter.


-Justin


On 19 Apr 2016, at 14:06, Justin Lemkul  wrote:


On 4/19/16 6:15 AM, gozde ergin wrote:

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k
   1 252.4 4184
   2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions.
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?


You may want to try this in CHARMM or NAMD, where it is quite honestly much 
easier.  All the specifications in GROMACS are relative to the initial 
configuration, and then there's refcoord_scaling to deal with, so I'm not 100% 
sure that this is as straightforward as it seems.  In CHARMM and NAMD, the 
positions of the walls are set explicitly and it is very straightforward to do 
these calculations.



Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?



It's the same.  This just means there's a harmonic potential at the wall.  The flat-bottom 
restraint says "apply a restraint potential if z > some value" and since there's a 
second restraint that applies a force if z < some value, each restraint covers half of a 
harmonic potential.

-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] semi-permeable wall in gromacs

[gozde ergin]

Is refcoord_scaling the issue for also NVT simulation? 
Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.

> On 19 Apr 2016, at 14:06, Justin Lemkul  wrote:
> 
> 
> On 4/19/16 6:15 AM, gozde ergin wrote:
>> This is my posre.itp file;
>> 
>> [ position_restraints ]
>> ; i  funct   gr(nm)   k
>>   1 252.4 4184
>>   2 252.4 4184
>> 
>> My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
>> the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 
>> 4.8-2.4=2.4nm
>> This step is working without any problem.
>> 
>> Than I use the command of;
>> 
>> gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy
>> 
>> I extract all ions z-coordinate of the ions.
>> Than I use the equation in Roux2010 paper in order to estimate the osmotic 
>> pressure which is,
>> 
>>  = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation 
>> only the ions who have passed the wall.
>>  = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)
>> 
>> Fwall = (Fwall1 + Fwall2)/2
>> P = /Area
>> 
>> However I get *very* different results than Roux2010. Even though our 
>> temperature, non-bond settings, system size etc are the same.
>> 
>> Has anyone here done simulations to calculate the osmotic pressure and/or 
>> osmotic coefficient?
>> Any suggestion?
> 
> You may want to try this in CHARMM or NAMD, where it is quite honestly much 
> easier.  All the specifications in GROMACS are relative to the initial 
> configuration, and then there's refcoord_scaling to deal with, so I'm not 
> 100% sure that this is as straightforward as it seems.  In CHARMM and NAMD, 
> the positions of the walls are set explicitly and it is very straightforward 
> to do these calculations.
> 
>> 
>> Also Roux2010 mentioned that the force of the wall is *half harmonic* , what 
>> is the force in gromacs for flat-bottom restraint?
>> 
> 
> It's the same.  This just means there's a harmonic potential at the wall.  
> The flat-bottom restraint says "apply a restraint potential if z > some 
> value" and since there's a second restraint that applies a force if z < some 
> value, each restraint covers half of a harmonic potential.
> 
> -Justin
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Re: [gmx-users] semi-permeable wall in gromacs

[Justin Lemkul]

On 4/19/16 6:15 AM, gozde ergin wrote:

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k
   1 252.4 4184
   2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions.
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?


You may want to try this in CHARMM or NAMD, where it is quite honestly much 
easier.  All the specifications in GROMACS are relative to the initial 
configuration, and then there's refcoord_scaling to deal with, so I'm not 100% 
sure that this is as straightforward as it seems.  In CHARMM and NAMD, the 
positions of the walls are set explicitly and it is very straightforward to do 
these calculations.




Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?



It's the same.  This just means there's a harmonic potential at the wall.  The 
flat-bottom restraint says "apply a restraint potential if z > some value" and 
since there's a second restraint that applies a force if z < some value, each 
restraint covers half of a harmonic potential.


-Justin




On 07 Apr 2016, at 21:37, Justin Lemkul  wrote:



On 4/7/16 12:57 PM, gozde ergin wrote:

Hi Justin,

I just want to ask how is the r(nm) in posre.itp working?

I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
box.

When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, 
it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 
nm.


This is expected.  The flat-bottom potential is established with respect to the 
reference coordinates.


But I do not want this, I would like to put a wall or force on +/-2.4 nm in z 
of the box.
Do you have any advice about this?



If you want walls at given z-values, the z-coordinate of species to which the 
restraint is applied have to be set to zero.  This coordinate file is passed to 
grompp -r as the reference point for the potential.

-Justin


Thanks in advance.



On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:



On 3/21/16 1:29 PM, gozde ergin wrote:

Ok this was a silly question.
In g_energy command 5. one is flat-bottom posres force.
Sorry.



The output of g_energy is energy, not force.

But the quantity is simple to calculate.  If you have applied a flat-bottom 
restraint along z, then you just need the time series of the z-coordinates of 
the restrained particles.

F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is 
active.  Since there are two walls, then you need to conditions, for +/- z0 and 
then the final sum should be divided by 2 before being divided by the area of 
the semipermeable wall.

-Justin


On 21 Mar 2016, at 17:26, gozde ergin  wrote:

Hey Justin,

I am just wondering in order to estimate the osmotic pressure I need extract 
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?

Thanks in advance




On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:



On 3/10/16 4:44 AM, gozde ergin wrote:

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules.
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?



So apply flat-bottom restraints to whatever the organic molecules are.  It's 
not something specific to ions.  You set the restraints in the molecule's 
topology (in its [moleculetype]), construct a reference coordinate file that 
defines some unphysical coordinates to be used as the center of the restraint, 
and that's it.  I've described the process in detail before so check the 
archive.

-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

==
--

Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k   
  1 252.4 4184
  2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions. 
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |) 

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?

Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?


> On 07 Apr 2016, at 21:37, Justin Lemkul  wrote:
> 
> 
> 
> On 4/7/16 12:57 PM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I just want to ask how is the r(nm) in posre.itp working?
>> 
>> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
>> box.
>> 
>> When I write 2.4 in the r(nm) property for [position_restraints] in 
>> posre.itp, it seems all of the molecules that I apply flat-bottom restraint 
>> travel +/- 2.4 nm.
> 
> This is expected.  The flat-bottom potential is established with respect to 
> the reference coordinates.
> 
>> But I do not want this, I would like to put a wall or force on +/-2.4 nm in 
>> z of the box.
>> Do you have any advice about this?
>> 
> 
> If you want walls at given z-values, the z-coordinate of species to which the 
> restraint is applied have to be set to zero.  This coordinate file is passed 
> to grompp -r as the reference point for the potential.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 3/21/16 1:29 PM, gozde ergin wrote:
 Ok this was a silly question.
 In g_energy command 5. one is flat-bottom posres force.
 Sorry.
 
>>> 
>>> The output of g_energy is energy, not force.
>>> 
>>> But the quantity is simple to calculate.  If you have applied a flat-bottom 
>>> restraint along z, then you just need the time series of the z-coordinates 
>>> of the restrained particles.
>>> 
>>> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint 
>>> is active.  Since there are two walls, then you need to conditions, for +/- 
>>> z0 and then the final sum should be divided by 2 before being divided by 
>>> the area of the semipermeable wall.
>>> 
>>> -Justin
>>> 
> On 21 Mar 2016, at 17:26, gozde ergin  wrote:
> 
> Hey Justin,
> 
> I am just wondering in order to estimate the osmotic pressure I need 
> extract the flat-bottom restraint force. (Force/Area = Pressure)
> Do you have any idea to how to extract this force?
> 
> Thanks in advance
> 
> 
> 
>> On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>> Dear Justin,
>>> 
>>> Thanks for your respond, I assume there is a way to apply this 
>>> restraint on specific molecules.
>>> Because my system is mixed with organic and water and I would like to 
>>> apply these forces on organic molecules not water?
>>> 
>> 
>> So apply flat-bottom restraints to whatever the organic molecules are.  
>> It's not something specific to ions.  You set the restraints in the 
>> molecule's topology (in its [moleculetype]), construct a reference 
>> coordinate file that defines some unphysical coordinates to be used as 
>> the center of the restraint, and that's it.  I've described the process 
>> in detail before so check the archive.
>> 
>> -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
>> 
>> ==
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>> posting!
>> 
>> * Can't post? Read 

Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Yes it worked. 
I appreciated to your help Justin.
Thanks a lot.

> On 07 Apr 2016, at 21:37, Justin Lemkul  wrote:
> 
> 
> 
> On 4/7/16 12:57 PM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I just want to ask how is the r(nm) in posre.itp working?
>> 
>> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
>> box.
>> 
>> When I write 2.4 in the r(nm) property for [position_restraints] in 
>> posre.itp, it seems all of the molecules that I apply flat-bottom restraint 
>> travel +/- 2.4 nm.
> 
> This is expected.  The flat-bottom potential is established with respect to 
> the reference coordinates.
> 
>> But I do not want this, I would like to put a wall or force on +/-2.4 nm in 
>> z of the box.
>> Do you have any advice about this?
>> 
> 
> If you want walls at given z-values, the z-coordinate of species to which the 
> restraint is applied have to be set to zero.  This coordinate file is passed 
> to grompp -r as the reference point for the potential.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 3/21/16 1:29 PM, gozde ergin wrote:
 Ok this was a silly question.
 In g_energy command 5. one is flat-bottom posres force.
 Sorry.
 
>>> 
>>> The output of g_energy is energy, not force.
>>> 
>>> But the quantity is simple to calculate.  If you have applied a flat-bottom 
>>> restraint along z, then you just need the time series of the z-coordinates 
>>> of the restrained particles.
>>> 
>>> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint 
>>> is active.  Since there are two walls, then you need to conditions, for +/- 
>>> z0 and then the final sum should be divided by 2 before being divided by 
>>> the area of the semipermeable wall.
>>> 
>>> -Justin
>>> 
> On 21 Mar 2016, at 17:26, gozde ergin  wrote:
> 
> Hey Justin,
> 
> I am just wondering in order to estimate the osmotic pressure I need 
> extract the flat-bottom restraint force. (Force/Area = Pressure)
> Do you have any idea to how to extract this force?
> 
> Thanks in advance
> 
> 
> 
>> On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>> Dear Justin,
>>> 
>>> Thanks for your respond, I assume there is a way to apply this 
>>> restraint on specific molecules.
>>> Because my system is mixed with organic and water and I would like to 
>>> apply these forces on organic molecules not water?
>>> 
>> 
>> So apply flat-bottom restraints to whatever the organic molecules are.  
>> It's not something specific to ions.  You set the restraints in the 
>> molecule's topology (in its [moleculetype]), construct a reference 
>> coordinate file that defines some unphysical coordinates to be used as 
>> the center of the restraint, and that's it.  I've described the process 
>> in detail before so check the archive.
>> 
>> -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
>> 
>> ==
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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 
>>>  
>>> >> >
>>> 
>>> ==
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at 

Re: [gmx-users] semi-permeable wall in gromacs

[Justin Lemkul]

On 4/7/16 12:57 PM, gozde ergin wrote:

Hi Justin,

I just want to ask how is the r(nm) in posre.itp working?

I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
box.

When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, 
it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 
nm.


This is expected.  The flat-bottom potential is established with respect to the 
reference coordinates.



But I do not want this, I would like to put a wall or force on +/-2.4 nm in z 
of the box.
Do you have any advice about this?



If you want walls at given z-values, the z-coordinate of species to which the 
restraint is applied have to be set to zero.  This coordinate file is passed to 
grompp -r as the reference point for the potential.


-Justin


Thanks in advance.



On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:



On 3/21/16 1:29 PM, gozde ergin wrote:

Ok this was a silly question.
In g_energy command 5. one is flat-bottom posres force.
Sorry.



The output of g_energy is energy, not force.

But the quantity is simple to calculate.  If you have applied a flat-bottom 
restraint along z, then you just need the time series of the z-coordinates of 
the restrained particles.

F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is 
active.  Since there are two walls, then you need to conditions, for +/- z0 and 
then the final sum should be divided by 2 before being divided by the area of 
the semipermeable wall.

-Justin


On 21 Mar 2016, at 17:26, gozde ergin  wrote:

Hey Justin,

I am just wondering in order to estimate the osmotic pressure I need extract 
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?

Thanks in advance




On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:



On 3/10/16 4:44 AM, gozde ergin wrote:

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules.
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?



So apply flat-bottom restraints to whatever the organic molecules are.  It's 
not something specific to ions.  You set the restraints in the molecule's 
topology (in its [moleculetype]), construct a reference coordinate file that 
defines some unphysical coordinates to be used as the center of the restraint, 
and that's it.  I've described the process in detail before so check the 
archive.

-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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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 


==
--
Gromacs Users mailing list

* Please search the archive at 
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 before posting!

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* For (un)subscribe requests visit
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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

==
--
Gromacs Users mailing list

* Please search the archive at 

Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Hi Justin,

I just want to ask how is the r(nm) in posre.itp working?

I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
box.

When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, 
it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 
nm.
But I do not want this, I would like to put a wall or force on +/-2.4 nm in z 
of the box.
Do you have any advice about this?

Thanks in advance.


> On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:
> 
> 
> 
> On 3/21/16 1:29 PM, gozde ergin wrote:
>> Ok this was a silly question.
>> In g_energy command 5. one is flat-bottom posres force.
>> Sorry.
>> 
> 
> The output of g_energy is energy, not force.
> 
> But the quantity is simple to calculate.  If you have applied a flat-bottom 
> restraint along z, then you just need the time series of the z-coordinates of 
> the restrained particles.
> 
> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is 
> active.  Since there are two walls, then you need to conditions, for +/- z0 
> and then the final sum should be divided by 2 before being divided by the 
> area of the semipermeable wall.
> 
> -Justin
> 
>>> On 21 Mar 2016, at 17:26, gozde ergin  wrote:
>>> 
>>> Hey Justin,
>>> 
>>> I am just wondering in order to estimate the osmotic pressure I need 
>>> extract the flat-bottom restraint force. (Force/Area = Pressure)
>>> Do you have any idea to how to extract this force?
>>> 
>>> Thanks in advance
>>> 
>>> 
>>> 
 On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:
 
 
 
 On 3/10/16 4:44 AM, gozde ergin wrote:
> Dear Justin,
> 
> Thanks for your respond, I assume there is a way to apply this restraint 
> on specific molecules.
> Because my system is mixed with organic and water and I would like to 
> apply these forces on organic molecules not water?
> 
 
 So apply flat-bottom restraints to whatever the organic molecules are.  
 It's not something specific to ions.  You set the restraints in the 
 molecule's topology (in its [moleculetype]), construct a reference 
 coordinate file that defines some unphysical coordinates to be used as the 
 center of the restraint, and that's it.  I've described the process in 
 detail before so check the archive.
 
 -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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>>> 
>> 
> 
> -- 
> ==
> 
> 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] semi-permeable wall in gromacs

[Justin Lemkul]

On 3/21/16 1:29 PM, gozde ergin wrote:

Ok this was a silly question.
In g_energy command 5. one is flat-bottom posres force.
Sorry.



The output of g_energy is energy, not force.

But the quantity is simple to calculate.  If you have applied a flat-bottom 
restraint along z, then you just need the time series of the z-coordinates of 
the restrained particles.


F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is 
active.  Since there are two walls, then you need to conditions, for +/- z0 and 
then the final sum should be divided by 2 before being divided by the area of 
the semipermeable wall.


-Justin


On 21 Mar 2016, at 17:26, gozde ergin  wrote:

Hey Justin,

I am just wondering in order to estimate the osmotic pressure I need extract 
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?

Thanks in advance




On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:



On 3/10/16 4:44 AM, gozde ergin wrote:

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules.
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?



So apply flat-bottom restraints to whatever the organic molecules are.  It's 
not something specific to ions.  You set the restraints in the molecule's 
topology (in its [moleculetype]), construct a reference coordinate file that 
defines some unphysical coordinates to be used as the center of the restraint, 
and that's it.  I've described the process in detail before so check the 
archive.

-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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--
==

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] semi-permeable wall in gromacs

[gozde ergin]

Ok this was a silly question. 
In g_energy command 5. one is flat-bottom posres force.
Sorry.

> On 21 Mar 2016, at 17:26, gozde ergin  wrote:
> 
> Hey Justin,
> 
> I am just wondering in order to estimate the osmotic pressure I need extract 
> the flat-bottom restraint force. (Force/Area = Pressure)
> Do you have any idea to how to extract this force?
> 
> Thanks in advance
> 
> 
> 
>> On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>> Dear Justin,
>>> 
>>> Thanks for your respond, I assume there is a way to apply this restraint on 
>>> specific molecules.
>>> Because my system is mixed with organic and water and I would like to apply 
>>> these forces on organic molecules not water?
>>> 
>> 
>> So apply flat-bottom restraints to whatever the organic molecules are.  It's 
>> not something specific to ions.  You set the restraints in the molecule's 
>> topology (in its [moleculetype]), construct a reference coordinate file that 
>> defines some unphysical coordinates to be used as the center of the 
>> restraint, and that's it.  I've described the process in detail before so 
>> check the archive.
>> 
>> -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
>> 
>> ==
>> -- 
>> Gromacs Users mailing list
>> 
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>> mail to gmx-users-requ...@gromacs.org.
> 

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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Hey Justin,

I am just wondering in order to estimate the osmotic pressure I need extract 
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?

Thanks in advance



> On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:
> 
> 
> 
> On 3/10/16 4:44 AM, gozde ergin wrote:
>> Dear Justin,
>> 
>> Thanks for your respond, I assume there is a way to apply this restraint on 
>> specific molecules.
>> Because my system is mixed with organic and water and I would like to apply 
>> these forces on organic molecules not water?
>> 
> 
> So apply flat-bottom restraints to whatever the organic molecules are.  It's 
> not something specific to ions.  You set the restraints in the molecule's 
> topology (in its [moleculetype]), construct a reference coordinate file that 
> defines some unphysical coordinates to be used as the center of the 
> restraint, and that's it.  I've described the process in detail before so 
> check the archive.
> 
> -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] semi-permeable wall in gromacs

[Justin Lemkul]

On 3/10/16 4:44 AM, gozde ergin wrote:

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules.
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?



So apply flat-bottom restraints to whatever the organic molecules are.  It's not 
something specific to ions.  You set the restraints in the molecule's topology 
(in its [moleculetype]), construct a reference coordinate file that defines some 
unphysical coordinates to be used as the center of the restraint, and that's it. 
 I've described the process in detail before so check the archive.


-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] semi-permeable wall in gromacs

[gozde ergin]

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules. 
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?

> On 09 Mar 2016, at 18:30, Justin Lemkul  wrote:
> 
> Use flat-bottom restraints on the ions

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Re: [gmx-users] semi-permeable wall in gromacs

[Justin Lemkul]

On 3/9/16 12:28 PM, gozde ergin wrote:

Dear all,

I would like to compute the osmotic pressure directly from all-atom MD 
simulations of concentrated aqueous solutions.

The basic idea is to introduce “virtual” walls to represent the effect of ideal 
semipermeable membranes, separating a high concentration region from a pure 
water region.

The walls keep the ions confined, but the water molecules are allowed to pass 
freely, permitting an equalization of their chemical potential throughout the 
entire system.

The mean force per unit area exerted on the ions by the virtual walls during 
the simulations can be directly related to the osmotic pressure.



My question is is there a way to introduce semi-permeable walls in GROMACS?



Use flat-bottom restraints on the ions.

-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] semi-permeable wall in gromacs

[gozde ergin]

Dear all,

I would like to compute the osmotic pressure directly from all-atom MD 
simulations of concentrated aqueous solutions. 

The basic idea is to introduce “virtual” walls to represent the effect of ideal 
semipermeable membranes, separating a high concentration region from a pure 
water region. 

The walls keep the ions confined, but the water molecules are allowed to pass 
freely, permitting an equalization of their chemical potential throughout the 
entire system. 

The mean force per unit area exerted on the ions by the virtual walls during 
the simulations can be directly related to the osmotic pressure. 



My question is is there a way to introduce semi-permeable walls in GROMACS?

bests
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