[gmx-users] Lipid bilayer moved apart
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 29 03:39:58 CEST 2009
You may find this post useful:
http://oldwww.gromacs.org/pipermail/gmx-users/2008-October/037571.html
-Justin
Bing Bing wrote:
> Dear All,
> I 've used steep for minimization for 50000 steps, but it converged in
> step 217, the final energy is as in previous email.
> here's the mdp file for em:-
> define = -DFLEXIBLE
> integrator = steep
> emtol = 1000
> emstep = 0.01
> nsteps = 50000
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> fourierspacing = 0.12
> rvdw = 0.9
> pme_order = 4
> ewald_rtol = 1e-5
> constraints= none
> As for the NVT, the mdp file is as below:-
> define = -DFLEXIBLE
> ; Run parameters
> integrator = md
> nsteps = 50000
> dt = 0.002
> ; Output control
> nstxout = 100
> nstvout = 100
> nstenergy = 100
> nstlog = 100
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 1
> lincs_order = 4
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist = 1.2
> rcoulomb = 1.2
> rvdw = 1.2
> ; Electrostatics
> coulombtype = PME
> pme_order = 4
> fourierspacing = 0.16
> ; Temperature coupling is on
> tcoupl = berendsen
> tc-grps = POPC SOL
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Pressure coupling is off
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres
> ; Velocity generation
> gen_vel = yes
> gen_temp = 323
> gen_seed = -1
>
> after the NVT, here;s the final energy:-
>
> Step Time Lambda
> 50000 100.00000 0.00000
>
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.073930 8799 8801 0.022445
> After LINCS 0.000039 8511 8513 0.000004
>
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
> 2.01361e+04 4.40814e+03 6.33528e+03 7.31363e+02 4.27554e+03
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 1.11735e+04 -1.01156e+04 -1.71631e+03 -1.65763e+05 -1.19549e+05
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -2.50084e+05 3.86207e+04 -2.11463e+05 3.03028e+02 -3.63528e+02
>
> as for the NPT, i ve used semiisotropic coupling for the pressure.
> Here's my nvt.mdp:-
>
> define = -DFLEXIBLE
> ; Run parameters
> integrator = md
> nsteps = 500000
> dt = 0.002
> ; Output control
> nstxout = 100
> nstvout = 100
> nstenergy = 100
> nstlog = 100
> ; Bond parameters
> continuation = yes
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 1
> lincs_order = 4
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist = 1.2
> rcoulomb = 1.2
> rvdw = 1.2
> ; Electrostatics
> coulombtype = PME
> pme_order = 4
> fourierspacing = 0.16
> ; Temperature coupling is on
> tcoupl = Nose-Hoover
> tc-grps = POPC SOL
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman
> pcoupltype = semiisotropic
> tau_p = 5.0
> ref_p = 1.0 1.0
> compressibility = 4.5e-5 4.5e-5
> ; Periodic boundary conditions
> pbc = xyz
> ; Dispersion correction
> DispCorr = EnerPres ;
> ; Velocity generation
> gen_vel = no ;
>
> it stopped at step 269 due to LINC warning as mentioned in the previous
> mail.
> Step 269, time 0.538 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 1980 and 1981) rms inf
> bonds that rotated more than 30 degrees:
>
> I ve checked the trajectory and the gap or space between both lipid
> layers is about 5 A away after the nvt simulation.
> Please advice.
>
> Regards,
> bing
>
>
>
>
> On Sun, Jun 28, 2009 at 10:37 PM, <shayamra at post.tau.ac.il
> <mailto:shayamra at post.tau.ac.il>> wrote:
>
> Greetings,
>
> Could you perhaps provide details of your energy minimization
> (conjugated? steep? etc.) and perhaps your mdp file for the
> simulation as well.
> What kind of pressure couplings did you use? (isotropic?
> semi-isotropic? etc.)
> How much further away did each layer move?
>
> I think it is usually recommended to simulate membranes with
> semi-isotropic pressure coupling, though I am not sure what is the
> cause of the error you are getting with NPT and LINCS.
>
> Regards,
> -Shay
>
>
> Quoting "Bing Bing" <jarbing09 at gmail.com <mailto:jarbing09 at gmail.com>>:
>
> Dear All,
> I'm simulating a empty membrane (128POPC + 2460 water) , the
> structure
> obtained from Tielemen's website.
> Thanks for the help from Justin and Mark, the structure had
> minimized and
> stop at 217steps
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Ryckaert-Bell.
> Improper Dih.
> 5.20262e+03 1.01146e+04 4.17230e+03 3.36598e+03
> 7.50236e+02
> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
> Coul. recip.
> 4.01104e+03 8.22333e+03 -1.49543e+04 -1.31978e+05
> -1.41296e+05
> Potential Kinetic En. Total Energy Temperature
> Pressure (bar)
> -2.52387e+05 0.00000e+00 -2.52387e+05 0.00000e+00
> 0.00000e+00
>
>
> Steepest Descents converged to Fmax < 1000 in 217 steps
> Potential Energy = -2.52387473541938e+05
> Maximum force = 9.30404466610315e+02 on atom 5631
> Norm of force = 5.34591310731597e+03
>
> The trajectory and energy seems ok.
>
> With this, i proceed with NVT, although by looking at the energy and
> temperature (300K) graph after NVT both looks fine. But when i
> tried to look
> at the trajectory, i noticed that the upper layer lipid and
> lower layer
> lapid actually moved further away from each other as compared to the
> starting structure. And i don't know what cause this to happen.
> Please
> advice.
> Subsequently, i moved on with NPT and it stopped due to LINCS
> warning as
> below:-
>
> Step 269, time 0.538 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 1980 and 1981) rms inf
> bonds that rotated more than 30 degrees:
>
> This mean that some of the atoms in the structure is moving and
> it is out of
> the cutt-off which being defined, it also said that it might due
> to the
> reason that the starting structure is not equilibrated or many
> overlaps. But
> as what i know,
> the structure is well equilibrated. What is the reason for this?
> Is it
> something which i missed out during NVT or NPT? Please advice.
>
>
> Regards,
> Bing
>
>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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