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, <shaya...@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" <jarbin...@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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