[gmx-users] How to fix interfacial tension in NPT
Souilem Safa
safasouilem1 at gmail.com
Thu Apr 25 15:10:51 CEST 2013
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 <safasouilem1 at gmail.com> wrote:
> Dear Justin,
> Thank you very much, that is very kind of you :)
>
>
>
> On 22 April 2013 19:42, Justin Lemkul <jalemkul at vt.edu> 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 <jalemkul at vt.edu> 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 = 250000 ; 2 *250000 = 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 <jalemkul at vt.edu> 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**<
>>>>>> http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>>>>>> >
>>>>>> <h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin<
>>>>>> http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>> >
>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ==============================******==========
>>>>>>
>>>>>>
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>>>>>> --
>>>> ==============================****==========
>>>>
>>>> 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<http://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>> >
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>> --
>> ==============================**==========
>>
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
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