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, <shaya...@post.tau.ac.il
<mailto: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 <mailto: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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--
========================================
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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