[gmx-users] How to fix interfacial tension in NPT
Souilem Safa
safasouilem1 at gmail.com
Mon Apr 22 13:48:25 CEST 2013
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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