[gmx-users] question about applying surface tension

Justin Lemkul jalemkul at vt.edu
Mon May 15 14:14:04 CEST 2017 


On 5/12/17 3:01 PM, Ali Shomali wrote:
> Dear Justin thanks for your answer
> actually I'm trying to reproduce other constant surface tension simulations
> of bilayers to make sure my method is right. they calculate area per lipid
> for different surface tensions from approximately 0 to 100 dyn/cm and that
> is why I've mdp files with different surface tension value . the thing that
> is confusing is that some papers have done simulation just for 2ns
>  doi:10.1021/jp048969n. and some other do the exact simulation in 50 ns
>  doi:10.1529/biophysj.105.065953.!

If you're trying to reproduce previous findings, do exactly what the authors did 
in terms of force field, cutoffs, time, etc. and if the results do not match, 
contact them to see what the reasons might be.  That's why corresponding authors 
exist.  I wouldn't trust results of membranes that were simulated for only 2 ns. 
  Just my opinion, but I seriously doubt that's enough time to equilibrate the 
systems.

> is constant surface tension applicable with other pressure coupling methods?

No idea, never tried it.  But I assume so.

-Justin

> thanks for your kind help
> Ali
>
> On Fri, May 12, 2017 at 9:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/12/17 12:27 PM, Ali Shomali wrote:
>>
>>> Dear Justin
>>> Is there any possibility that the cause of problem is my simulation time ?
>>> (3 ns)
>>>
>>>
>> Yes, that's about 50 times too short to be credible.  Lipids relax over
>> tens of nanoseconds, and typical production run times for well equilibrated
>> membrane systems are over 100 ns.
>>
>> Additionally, Berendsen methods do not produce correct ensembles, and
>> you're specifying zero surface tension in x-y.  Is that really what you
>> want?  You've shown very different .mdp files, one with 600 bar of
>> compression claiming surface tension, now this.  I'm just not even clear
>> what you're really doing.
>>
>> -Justin
>>
>>
>> On Mon, May 8, 2017 at 4:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 5/7/17 2:56 PM, Ali Shomali wrote:
>>>>
>>>> Thanks so much Justin for your answer. actually I performed different
>>>>> simulations and compared the area per lipid with existing studies . for
>>>>> example I used gromacs charmm 22 for DPPC simulation and compared the
>>>>> results with Dr.Feller's paper. also I conducted a simulation on DMPC
>>>>> membrane and compared the results with existing data from
>>>>>  doi:10.1021/jp048969n. also I performed a simulation with gromacs opls
>>>>> force field on octadecanol monolayer and  checked the results with
>>>>>  doi:10.1016/j.colsurfa.2012.09.025. in all of them my area per lipid
>>>>> value
>>>>> changes very little and another odd thing is that even when I apply a
>>>>> large
>>>>> surface tension , surface compresses!
>>>>>
>>>>>
>>>> You're sort of indirectly applying a surface tension.  You've got an x-y
>>>> pressure of 600 bar, which means the membrane will be squeezed under the
>>>> influence of high pressure.  Note that there are actual surface tension
>>>> options that you should probably be using.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> I've tested all the option I could think of.
>>>>
>>>>> I would appreciate it so much  if you can help me with this problem
>>>>> Justin
>>>>> thanks again
>>>>> Ali
>>>>>
>>>>> On Sun, May 7, 2017 at 10:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 5/6/17 6:58 PM, Ali Shomali wrote:
>>>>>>
>>>>>> Hello to all dear gromacs users
>>>>>>
>>>>>>>
>>>>>>> I've faced a problem with applying surface tension , I'm , trying to
>>>>>>> model
>>>>>>> a monolayer and I've noticed whenever I apply a surface tension
>>>>>>> although
>>>>>>> my
>>>>>>> surface tension is converged  my area per lipid is wrong . i managed
>>>>>>> to
>>>>>>> model a bilayer to find out the problem and i noticed that in all my
>>>>>>> simulations my area per lipid changes are very little no matter what
>>>>>>> is
>>>>>>> surface tension nor cutoffs. but surface tension converges! i'm
>>>>>>> sending
>>>>>>> my
>>>>>>> mdp file .
>>>>>>> I will be so thankful if some one helps
>>>>>>>
>>>>>>>
>>>>>>> Sounds like a force field issue.  Which parameter set are you using,
>>>>>> and
>>>>>> do you have evidence that it should respond correctly under such
>>>>>> conditions?
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>  mdp file :
>>>>>>
>>>>>>
>>>>>>> title = DMPC NPT equilibration
>>>>>>> ; Run parameters
>>>>>>> integrator = md ; leap-frog integrator
>>>>>>> nsteps = 1000000 ; = 1000 ps
>>>>>>> dt = 0.001 ; 1 fs
>>>>>>> nstcomm                  = 10
>>>>>>> comm-grps                = SOL DMPC ; Remove COM for monolayers
>>>>>>> separately
>>>>>>> ; Output control
>>>>>>> nstxout = 10000 ; save coordinates every 1.0 ps
>>>>>>> nstvout = 10000 ; save velocities every 1.0 ps
>>>>>>> nstenergy = 500 ; save energies every 1.0 ps
>>>>>>> nstlog = 500 ; update log file every 1.0 ps
>>>>>>>
>>>>>>> ; Neighborsearching
>>>>>>> cutoff-scheme   = Verlet
>>>>>>> ns_type     = grid ; search neighboring grid cells
>>>>>>> nstlist     = 10 ; 20 fs, largely irrelevant with Verlet
>>>>>>> rcoulomb     = 1.4 ; short-range electrostatic cutoff (in nm)
>>>>>>> rvdw     = 1.4 ; short-range van der Waals cutoff (in nm)
>>>>>>> ; Dispersion correction
>>>>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>>>>> ; Electrostatics
>>>>>>> coulombtype     = PME ; Particle Mesh Ewald for long-range
>>>>>>> electrostatics
>>>>>>> ; Temperature coupling is on
>>>>>>> tcoupl = berendsen             ; modified Berendsen thermostat
>>>>>>> tc-grps = DMPC SOL ; two coupling groups - more accurate
>>>>>>> tau_t = 0.1   0.1           ; time constant, in ps
>>>>>>> ref_t = 330    330           ; reference temperature, one for each
>>>>>>> group,
>>>>>>> in K
>>>>>>> ; Pressure coupling is on
>>>>>>> Pcoupl = berendsen
>>>>>>> tau_p = 10.0
>>>>>>> compressibility = 4.5e-5 4.5e-5
>>>>>>> ref_p = 600 1.0
>>>>>>> ; Periodic boundary conditions
>>>>>>> pbc = xyz     ; 3-D PBC
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> 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
>>>>>>
>>>>>> jalemkul at 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
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
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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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

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