Dear Justin thanks for the answer I think the surface tension line was deleted in email by mistake , sorry for that. I managed to perform other simulations for DMPC and DPPC . in all of them I applied reported surface tensions ( twice the reported surface tension per interface) in all of them my area per lipid changes very little and it's very confusing becuase I compared my mdp script with others from internet , I'm sending my mdp options again (nstcomm is added): title = NGT Equilibration for DPPC ; Run parameters integrator = md ; leap-frog integrator nsteps = 1000000 ; 1000 ps (1 ns) dt = 0.001 ; 2 fs ; Output control nstxout = 10000 ; save coordinates every 0.2 ps nstvout = 10000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps
; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation ; Temperature coupling is on tcoupl = berendsen ; More accurate thermostat tc-grps = DPPC SOL ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = berendsen ; Pressure coupling on in NPT tau_p = 5.0 ; time constant, in ps ref_p = 0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 pcoupltype = surface-tension ; ; 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 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 100 comm-mode = Linear comm-grps = system On Mon, May 8, 2017 at 4:38 PM, Justin Lemkul <jalem...@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 <jalem...@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 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > 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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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