Dear Justin, Thank you very much, that is very kind of you :)
On 22 April 2013 19:42, Justin Lemkul <jalem...@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 <jalem...@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 <jalem...@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> >>>>> > >>>>> >>>>>> >>>>>> >>>>> ==============================******========== >>>>> >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@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> >>>>> > >>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> >>>>> >>>>> Mailing_Lists/Search<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-requ...@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> >>>>> > >>>>> <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://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@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-requ...@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@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-requ...@gromacs.org. > * Can't post? 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