Re: [gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Thank you for your reply :) I will look further


On 25 April 2013 23:18, Justin Lemkul  wrote:

>
>
> On 4/25/13 9:10 AM, Souilem Safa wrote:
>
>> Dear Justin,
>> Please I want to ask you for the calculation of interfacial tension from
>> the formula : 1/2 (Pz - (px+py)/2))*Lz
>> Should I calculate the interfacial tension in every step and take the
>> average interfacial tension for all the steps or should I take the average
>> of the presssure tensors from all the steps and calculate the interfacial
>> tension which will be only one value? Because it gives different values.
>>
>
> Beyond my area of expertise.  Maybe someone who does this kind of work can
> answer this.
>
> -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!
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Re: [gmx-users] How to fix interfacial tension in NPT

[Justin Lemkul]

On 4/25/13 9:10 AM, Souilem Safa wrote:

Dear Justin,
Please I want to ask you for the calculation of interfacial tension from
the formula : 1/2 (Pz - (px+py)/2))*Lz
Should I calculate the interfacial tension in every step and take the
average interfacial tension for all the steps or should I take the average
of the presssure tensors from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.


Beyond my area of expertise.  Maybe someone who does this kind of work can 
answer this.


-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

Re: [gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Dear Justin,
Please I want to ask you for the calculation of interfacial tension from
the formula : 1/2 (Pz - (px+py)/2))*Lz
Should I calculate the interfacial tension in every step and take the
average interfacial tension for all the steps or should I take the average
of the presssure tensors from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.
Thank you very much


On 22 April 2013 20:48, Souilem Safa  wrote:

> Dear Justin,
> Thank you very much, that is very kind of you :)
>
>
>
> On 22 April 2013 19:42, Justin Lemkul  wrote:
>
>>
>>
>> On 4/21/13 10:37 PM, Souilem Safa wrote:
>>
>>> Dear Justin,
>>>
>>> Thanks for your quick reply.
>>> I used Gromos 96 force field, I found it well reproduce triglycerides
>>> properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is
>>> the
>>> updated one but I'm not sure if it well reproduce the the surface tension
>>> properties . I found recently one paper simulating
>>> triglyceride-phospholipid-**water membrane (G. Henneré et al., 2009),
>>> they
>>> use united atom force field for simulation.
>>> Which force field do you think it is better , I'm sorry I have limited
>>> knowledge about it since I'm just beginner  in MD simulation.
>>>
>>
>> My advice would be to find a study that has been shown to produce the
>> types of data you are interested in, then try to reproduce it exactly.  If
>> you can do that, move on to your systems using the same force field.  Only
>> then can you sort out whether your results are due to some error that you
>> are making (and I did note an important mistake below) or due to the
>> limitations of the force field itself.
>>
>> -Justin
>>
>>  On 22 April 2013 10:37, Justin Lemkul  wrote:
>>>
>>>

 On 4/21/13 9:30 PM, Souilem Safa wrote:

  Dear Justin,
> Thank you for your answer, I'm sorry for delay to reply. Actually I'm
> running a simulation of oil-water interface. I'm using Gromos 53a6
> force
> field which is usually used for triglycerides. after semiisotropic and
> MD
> step I still have around 40 mN.m-1 interfacial tension which is pretty
> far
> from my experimental value. Following is my mdp file for NPT step.
> I would be very grateful if you can help me to solve this issue
>
>
 Do you have any reason to believe that 53A6 should reproduce quantities
 like surface tension?  I haven't seen such a demonstration before,
 though I
 admit I haven't actively gone looking.  The cutoffs you are using are
 incorrect for strict use of 53A6; that could be a contributing factor to
 your problems.

 -Justin

   title   = NPT equilibration

> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 25; 2 *25 = 500 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 500   ; save coordinates every 1 ps
> nstvout = 100   ; save velocities every 0.2 ps
> nstenergy   = 100   ; save energies every 0.2 ps
> nstlog  = 100   ; update log file every 0.2 ps
> ; Bond parameters
> continuation= yes   ; Restarting after NVT
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 2 ; accuracy of LINCS
> lincs_order = 2 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist   = 1.0   ; short-range neighborlist cutoff (in
> nm)
> rcoulomb= 1.0   ; short-range electrostatic cutoff (in
> nm)
> rvdw= 1.0   ; short-range van der Waals cutoff (in
> nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc-grps = SOL TRI   ; two coupling groups - more accurate
> tau_t   = 0.1 0.1   ; time constant, in ps
> ref_t   = 300 300   ; reference temperature, one for each
> group, in K
> ; Pressure coupling is on
> pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype  = semiisotropic ; uniform scaling of box
> vectors
> tau_p   = 1.0 1.0   ; time constant, in ps
> ref_p   = 1.0 1.0   ; reference pressure, in bar
> compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
> axis

Re: [gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Dear Justin,
Thank you very much, that is very kind of you :)



On 22 April 2013 19:42, Justin Lemkul  wrote:

>
>
> On 4/21/13 10:37 PM, Souilem Safa wrote:
>
>> Dear Justin,
>>
>> Thanks for your quick reply.
>> I used Gromos 96 force field, I found it well reproduce triglycerides
>> properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is the
>> updated one but I'm not sure if it well reproduce the the surface tension
>> properties . I found recently one paper simulating
>> triglyceride-phospholipid-**water membrane (G. Henneré et al., 2009),
>> they
>> use united atom force field for simulation.
>> Which force field do you think it is better , I'm sorry I have limited
>> knowledge about it since I'm just beginner  in MD simulation.
>>
>
> My advice would be to find a study that has been shown to produce the
> types of data you are interested in, then try to reproduce it exactly.  If
> you can do that, move on to your systems using the same force field.  Only
> then can you sort out whether your results are due to some error that you
> are making (and I did note an important mistake below) or due to the
> limitations of the force field itself.
>
> -Justin
>
>  On 22 April 2013 10:37, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/21/13 9:30 PM, Souilem Safa wrote:
>>>
>>>  Dear Justin,
 Thank you for your answer, I'm sorry for delay to reply. Actually I'm
 running a simulation of oil-water interface. I'm using Gromos 53a6 force
 field which is usually used for triglycerides. after semiisotropic and
 MD
 step I still have around 40 mN.m-1 interfacial tension which is pretty
 far
 from my experimental value. Following is my mdp file for NPT step.
 I would be very grateful if you can help me to solve this issue


>>> Do you have any reason to believe that 53A6 should reproduce quantities
>>> like surface tension?  I haven't seen such a demonstration before,
>>> though I
>>> admit I haven't actively gone looking.  The cutoffs you are using are
>>> incorrect for strict use of 53A6; that could be a contributing factor to
>>> your problems.
>>>
>>> -Justin
>>>
>>>   title   = NPT equilibration
>>>
 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 25; 2 *25 = 500 ps
 dt  = 0.002 ; 2 fs
 ; Output control
 nstxout = 500   ; save coordinates every 1 ps
 nstvout = 100   ; save velocities every 0.2 ps
 nstenergy   = 100   ; save energies every 0.2 ps
 nstlog  = 100   ; update log file every 0.2 ps
 ; Bond parameters
 continuation= yes   ; Restarting after NVT
 constraint_algorithm = lincs; holonomic constraints
 constraints = all-bonds ; all bonds (even heavy atom-H bonds)
 constrained
 lincs_iter  = 2 ; accuracy of LINCS
 lincs_order = 2 ; also related to accuracy
 ; Neighborsearching
 ns_type = grid  ; search neighboring grid cells
 nstlist = 5 ; 10 fs
 rlist   = 1.0   ; short-range neighborlist cutoff (in
 nm)
 rcoulomb= 1.0   ; short-range electrostatic cutoff (in
 nm)
 rvdw= 1.0   ; short-range van der Waals cutoff (in
 nm)
 ; Electrostatics
 coulombtype = PME   ; Particle Mesh Ewald for long-range
 electrostatics
 pme_order   = 4 ; cubic interpolation
 fourierspacing  = 0.16  ; grid spacing for FFT
 ; Temperature coupling is on
 tcoupl  = V-rescale ; modified Berendsen thermostat
 tc-grps = SOL TRI   ; two coupling groups - more accurate
 tau_t   = 0.1 0.1   ; time constant, in ps
 ref_t   = 300 300   ; reference temperature, one for each
 group, in K
 ; Pressure coupling is on
 pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
 pcoupltype  = semiisotropic ; uniform scaling of box vectors
 tau_p   = 1.0 1.0   ; time constant, in ps
 ref_p   = 1.0 1.0   ; reference pressure, in bar
 compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
 axis bar^-1
 refcoord_scaling = com
 ; Periodic boundary conditions
 pbc = xyz   ; 3-D PBC
 ; Dispersion correction
 DispCorr= enerpres  ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel = no; Velocity generation is off




 On 19 April 2013 03:28, Justin Lemkul  wrote:



> On 4/18/13 10:51 AM, Souilem Safa wrote:
>
>   Dear Gromacs users,
>
>> I have runned a semiisotropic NPT simulation for a membrane, I have
>> fixed
>> the pressure in x and y axis a

Re: [gmx-users] How to fix interfacial tension in NPT

[Justin Lemkul]

On 4/21/13 10:37 PM, Souilem Safa wrote:

Dear Justin,
Thanks for your quick reply.
I used Gromos 96 force field, I found it well reproduce triglycerides
properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is the
updated one but I'm not sure if it well reproduce the the surface tension
properties . I found recently one paper simulating
triglyceride-phospholipid-water membrane (G. Henneré et al., 2009), they
use united atom force field for simulation.
Which force field do you think it is better , I'm sorry I have limited
knowledge about it since I'm just beginner  in MD simulation.


My advice would be to find a study that has been shown to produce the types of 
data you are interested in, then try to reproduce it exactly.  If you can do 
that, move on to your systems using the same force field.  Only then can you 
sort out whether your results are due to some error that you are making (and I 
did note an important mistake below) or due to the limitations of the force 
field itself.


-Justin


On 22 April 2013 10:37, Justin Lemkul  wrote:




On 4/21/13 9:30 PM, Souilem Safa wrote:


Dear Justin,
Thank you for your answer, I'm sorry for delay to reply. Actually I'm
running a simulation of oil-water interface. I'm using Gromos 53a6 force
field which is usually used for triglycerides. after semiisotropic and MD
step I still have around 40 mN.m-1 interfacial tension which is pretty far
from my experimental value. Following is my mdp file for NPT step.
I would be very grateful if you can help me to solve this issue



Do you have any reason to believe that 53A6 should reproduce quantities
like surface tension?  I haven't seen such a demonstration before, though I
admit I haven't actively gone looking.  The cutoffs you are using are
incorrect for strict use of 53A6; that could be a contributing factor to
your problems.

-Justin

  title   = NPT equilibration

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 25; 2 *25 = 500 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 2 ; accuracy of LINCS
lincs_order = 2 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = SOL TRI   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of box vectors
tau_p   = 1.0 1.0   ; time constant, in ps
ref_p   = 1.0 1.0   ; reference pressure, in bar
compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
axis bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= enerpres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off




On 19 April 2013 03:28, Justin Lemkul  wrote:




On 4/18/13 10:51 AM, Souilem Safa wrote:

  Dear Gromacs users,

I have runned a semiisotropic NPT simulation for a membrane, I have
fixed
the pressure in x and y axis and I varied it only in z axis to keep a
stable interface. But after simulation the obtained interfacial tension
is
far bigger than the experimental value. Experimental is 27 mN.m-1 and
the
simulated one was around 38 mN.m-1.
I will be very grateful if you can suggest me which parameters should I
check in order to regulate the interfacial tension value.



You haven't posted your .mdp file or even stated what force field you're
using.  Is your force field designed to reproduce such surface tension
values?  The results are only as good as the model itself, and your usage
of it.

-Justin

--
===

Re: [gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Dear Justin,
Thanks for your quick reply.
I used Gromos 96 force field, I found it well reproduce triglycerides
properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is the
updated one but I'm not sure if it well reproduce the the surface tension
properties . I found recently one paper simulating
triglyceride-phospholipid-water membrane (G. Henneré et al., 2009), they
use united atom force field for simulation.
Which force field do you think it is better , I'm sorry I have limited
knowledge about it since I'm just beginner  in MD simulation.
Many thanks



On 22 April 2013 10:37, Justin Lemkul  wrote:

>
>
> On 4/21/13 9:30 PM, Souilem Safa wrote:
>
>> Dear Justin,
>> Thank you for your answer, I'm sorry for delay to reply. Actually I'm
>> running a simulation of oil-water interface. I'm using Gromos 53a6 force
>> field which is usually used for triglycerides. after semiisotropic and MD
>> step I still have around 40 mN.m-1 interfacial tension which is pretty far
>> from my experimental value. Following is my mdp file for NPT step.
>> I would be very grateful if you can help me to solve this issue
>>
>
> Do you have any reason to believe that 53A6 should reproduce quantities
> like surface tension?  I haven't seen such a demonstration before, though I
> admit I haven't actively gone looking.  The cutoffs you are using are
> incorrect for strict use of 53A6; that could be a contributing factor to
> your problems.
>
> -Justin
>
>  title   = NPT equilibration
>> ; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 25; 2 *25 = 500 ps
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 500   ; save coordinates every 1 ps
>> nstvout = 100   ; save velocities every 0.2 ps
>> nstenergy   = 100   ; save energies every 0.2 ps
>> nstlog  = 100   ; update log file every 0.2 ps
>> ; Bond parameters
>> continuation= yes   ; Restarting after NVT
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 2 ; accuracy of LINCS
>> lincs_order = 2 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl  = V-rescale ; modified Berendsen thermostat
>> tc-grps = SOL TRI   ; two coupling groups - more accurate
>> tau_t   = 0.1 0.1   ; time constant, in ps
>> ref_t   = 300 300   ; reference temperature, one for each
>> group, in K
>> ; Pressure coupling is on
>> pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
>> pcoupltype  = semiisotropic ; uniform scaling of box vectors
>> tau_p   = 1.0 1.0   ; time constant, in ps
>> ref_p   = 1.0 1.0   ; reference pressure, in bar
>> compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
>> axis bar^-1
>> refcoord_scaling = com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= enerpres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = no; Velocity generation is off
>>
>>
>>
>>
>> On 19 April 2013 03:28, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/13 10:51 AM, Souilem Safa wrote:
>>>
>>>  Dear Gromacs users,
 I have runned a semiisotropic NPT simulation for a membrane, I have
 fixed
 the pressure in x and y axis and I varied it only in z axis to keep a
 stable interface. But after simulation the obtained interfacial tension
 is
 far bigger than the experimental value. Experimental is 27 mN.m-1 and
 the
 simulated one was around 38 mN.m-1.
 I will be very grateful if you can suggest me which parameters should I
 check in order to regulate the interfacial tension value.


>>> You haven't posted your .mdp file or even stated what force field you're
>>> using.  Is your force field designed to reproduce such surface tension
>>> values?  The results are only as good as the model itself, and your usage
>>> of it.
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>>

Re: [gmx-users] How to fix interfacial tension in NPT

[Justin Lemkul]

On 4/21/13 9:30 PM, Souilem Safa wrote:

Dear Justin,
Thank you for your answer, I'm sorry for delay to reply. Actually I'm
running a simulation of oil-water interface. I'm using Gromos 53a6 force
field which is usually used for triglycerides. after semiisotropic and MD
step I still have around 40 mN.m-1 interfacial tension which is pretty far
from my experimental value. Following is my mdp file for NPT step.
I would be very grateful if you can help me to solve this issue


Do you have any reason to believe that 53A6 should reproduce quantities like 
surface tension?  I haven't seen such a demonstration before, though I admit I 
haven't actively gone looking.  The cutoffs you are using are incorrect for 
strict use of 53A6; that could be a contributing factor to your problems.


-Justin


title   = NPT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 25; 2 *25 = 500 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 2 ; accuracy of LINCS
lincs_order = 2 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = SOL TRI   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of box vectors
tau_p   = 1.0 1.0   ; time constant, in ps
ref_p   = 1.0 1.0   ; reference pressure, in bar
compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
axis bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= enerpres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off




On 19 April 2013 03:28, Justin Lemkul  wrote:




On 4/18/13 10:51 AM, Souilem Safa wrote:


Dear Gromacs users,
I have runned a semiisotropic NPT simulation for a membrane, I have fixed
the pressure in x and y axis and I varied it only in z axis to keep a
stable interface. But after simulation the obtained interfacial tension is
far bigger than the experimental value. Experimental is 27 mN.m-1 and the
simulated one was around 38 mN.m-1.
I will be very grateful if you can suggest me which parameters should I
check in order to regulate the interfacial tension value.



You haven't posted your .mdp file or even stated what force field you're
using.  Is your force field designed to reproduce such surface tension
values?  The results are only as good as the model itself, and your usage
of it.

-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://w

Re: [gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Dear Justin,
Thank you for your answer, I'm sorry for delay to reply. Actually I'm
running a simulation of oil-water interface. I'm using Gromos 53a6 force
field which is usually used for triglycerides. after semiisotropic and MD
step I still have around 40 mN.m-1 interfacial tension which is pretty far
from my experimental value. Following is my mdp file for NPT step.
I would be very grateful if you can help me to solve this issue
title   = NPT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 25; 2 *25 = 500 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 2 ; accuracy of LINCS
lincs_order = 2 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = SOL TRI   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of box vectors
tau_p   = 1.0 1.0   ; time constant, in ps
ref_p   = 1.0 1.0   ; reference pressure, in bar
compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
axis bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= enerpres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off




On 19 April 2013 03:28, Justin Lemkul  wrote:

>
>
> On 4/18/13 10:51 AM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>> I have runned a semiisotropic NPT simulation for a membrane, I have fixed
>> the pressure in x and y axis and I varied it only in z axis to keep a
>> stable interface. But after simulation the obtained interfacial tension is
>> far bigger than the experimental value. Experimental is 27 mN.m-1 and the
>> simulated one was around 38 mN.m-1.
>> I will be very grateful if you can suggest me which parameters should I
>> check in order to regulate the interfacial tension value.
>>
>
> You haven't posted your .mdp file or even stated what force field you're
> using.  Is your force field designed to reproduce such surface tension
> values?  The results are only as good as the model itself, and your usage
> of it.
>
> -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
>
> ==**==
> --
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Re: [gmx-users] How to fix interfacial tension in NPT

[Justin Lemkul]

On 4/18/13 10:51 AM, Souilem Safa wrote:

Dear Gromacs users,
I have runned a semiisotropic NPT simulation for a membrane, I have fixed
the pressure in x and y axis and I varied it only in z axis to keep a
stable interface. But after simulation the obtained interfacial tension is
far bigger than the experimental value. Experimental is 27 mN.m-1 and the
simulated one was around 38 mN.m-1.
I will be very grateful if you can suggest me which parameters should I
check in order to regulate the interfacial tension value.


You haven't posted your .mdp file or even stated what force field you're using. 
 Is your force field designed to reproduce such surface tension values?  The 
results are only as good as the model itself, and your usage of it.


-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


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[gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Dear Gromacs users,
I have runned a semiisotropic NPT simulation for a membrane, I have fixed
the pressure in x and y axis and I varied it only in z axis to keep a
stable interface. But after simulation the obtained interfacial tension is
far bigger than the experimental value. Experimental is 27 mN.m-1 and the
simulated one was around 38 mN.m-1.
I will be very grateful if you can suggest me which parameters should I
check in order to regulate the interfacial tension value.
Thank you very much
-- 
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