[gmx-users] Lipid bilayer moved apart

Bing Bing jarbing09 at gmail.com
Mon Jun 29 03:25:09 CEST 2009


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> 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>:
>
>  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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