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

Mon Apr 22 04:37:58 CEST 2013

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 <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>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ==============================****==========
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<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-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<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://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>