Dear All,<br>I 've used steep for minimization for 50000 steps, but it converged in step 217, the final energy is as in previous email.<br>here's the mdp file for em:-<br>define = -DFLEXIBLE<br>integrator = steep<br>
emtol = 1000<br>emstep = 0.01<br>nsteps = 50000<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>fourierspacing = 0.12<br>rvdw = 0.9<br>pme_order = 4<br>ewald_rtol = 1e-5<br>constraints= none<br> As for the NVT, the mdp file is as below:-<br>
define = -DFLEXIBLE <br>; Run parameters<br>integrator = md <br>nsteps = 50000 <br>dt = 0.002 <br>; Output control<br>nstxout = 100 <br>nstvout = 100 <br>
nstenergy = 100 <br>nstlog = 100 <br>; Bond parameters<br>continuation = no <br>constraint_algorithm = lincs <br>constraints = all-bonds <br>lincs_iter = 1 <br>
lincs_order = 4 <br>; Neighborsearching<br>ns_type = grid <br>nstlist = 5 <br>rlist = 1.2 <br>rcoulomb = 1.2 <br>rvdw = 1.2 <br>
; Electrostatics<br>coulombtype = PME <br>pme_order = 4 <br>fourierspacing = 0.16 <br>; Temperature coupling is on<br>tcoupl = berendsen <br>tc-grps = POPC SOL <br>
tau_t = 0.1 0.1 <br>ref_t = 300 300 <br>; Pressure coupling is off<br>pcoupl = no ; no pressure coupling in NVT<br>; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>DispCorr = EnerPres <br>; Velocity generation<br>gen_vel = yes <br>gen_temp = 323 <br>gen_seed = -1 <br><br>after the NVT, here;s the final energy:- <br>
<br> Step Time Lambda<br> 50000 100.00000 0.00000<br><br> Rel. Constraint Deviation: Max between atoms RMS<br> Before LINCS 0.073930 8799 8801 0.022445<br>
After LINCS 0.000039 8511 8513 0.000004<br><br> Energies (kJ/mol)<br> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<br> 2.01361e+04 4.40814e+03 6.33528e+03 7.31363e+02 4.27554e+03<br>
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.<br> 1.11735e+04 -1.01156e+04 -1.71631e+03 -1.65763e+05 -1.19549e+05<br> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br>
-2.50084e+05 3.86207e+04 -2.11463e+05 3.03028e+02 -3.63528e+02<br><br>as for the NPT, i ve used semiisotropic coupling for the pressure. Here's my nvt.mdp:-<br><br>define = -DFLEXIBLE <br>; Run parameters<br>
integrator = md <br>nsteps = 500000 <br>dt = 0.002 <br>; Output control<br>nstxout = 100 <br>nstvout = 100 <br>nstenergy = 100 <br>
nstlog = 100 <br>; Bond parameters<br>continuation = yes <br>constraint_algorithm = lincs <br>constraints = all-bonds <br>lincs_iter = 1 <br>lincs_order = 4 <br>
; Neighborsearching<br>ns_type = grid <br>nstlist = 5 <br>rlist = 1.2 <br>rcoulomb = 1.2 <br>rvdw = 1.2 <br>; Electrostatics<br>coulombtype = PME <br>
pme_order = 4 <br>fourierspacing = 0.16 <br>; Temperature coupling is on<br>tcoupl = Nose-Hoover <br>tc-grps = POPC SOL <br>tau_t = 0.1 0.1 <br>ref_t = 300 300 <br>
; Pressure coupling is on<br>pcoupl = Parrinello-Rahman <br>pcoupltype = semiisotropic <br>tau_p = 5.0 <br>ref_p = 1.0 1.0 <br>compressibility = 4.5e-5 4.5e-5 <br>
; Periodic boundary conditions<br>pbc = xyz <br>; Dispersion correction<br>DispCorr = EnerPres ;<br>; Velocity generation<br>gen_vel = no ;<br><br>it stopped at step 269 due to LINC warning as mentioned in the previous mail.<br>
Step 269, time 0.538 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max inf (between atoms 1980 and 1981) rms inf<br>bonds that rotated more than 30 degrees:<br><br>I ve checked the trajectory and the gap or space between both lipid layers is about 5 A away after the nvt simulation.<br>
Please advice.<br><br>Regards,<br>bing<br><br><br><br><br><div class="gmail_quote">On Sun, Jun 28, 2009 at 10:37 PM, <span dir="ltr"><<a href="mailto:shayamra@post.tau.ac.il">shayamra@post.tau.ac.il</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Greetings,<br>
<br>
Could you perhaps provide details of your energy minimization (conjugated? steep? etc.) and perhaps your mdp file for the simulation as well.<br>
What kind of pressure couplings did you use? (isotropic? semi-isotropic? etc.)<br>
How much further away did each layer move?<br>
<br>
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.<br>
<br>
Regards,<br>
-Shay<div><div></div><div class="h5"><br>
<br>
Quoting "Bing Bing" <<a href="mailto:jarbing09@gmail.com" target="_blank">jarbing09@gmail.com</a>>:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All,<br>
I'm simulating a empty membrane (128POPC + 2460 water) , the structure<br>
obtained from Tielemen's website.<br>
Thanks for the help from Justin and Mark, the structure had minimized and<br>
stop at 217steps<br>
<br>
Energies (kJ/mol)<br>
Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br>
5.20262e+03 1.01146e+04 4.17230e+03 3.36598e+03 7.50236e+02<br>
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.<br>
4.01104e+03 8.22333e+03 -1.49543e+04 -1.31978e+05 -1.41296e+05<br>
Potential Kinetic En. Total Energy Temperature Pressure (bar)<br>
-2.52387e+05 0.00000e+00 -2.52387e+05 0.00000e+00 0.00000e+00<br>
<br>
<br>
Steepest Descents converged to Fmax < 1000 in 217 steps<br>
Potential Energy = -2.52387473541938e+05<br>
Maximum force = 9.30404466610315e+02 on atom 5631<br>
Norm of force = 5.34591310731597e+03<br>
<br>
The trajectory and energy seems ok.<br>
<br>
With this, i proceed with NVT, although by looking at the energy and<br>
temperature (300K) graph after NVT both looks fine. But when i tried to look<br>
at the trajectory, i noticed that the upper layer lipid and lower layer<br>
lapid actually moved further away from each other as compared to the<br>
starting structure. And i don't know what cause this to happen. Please<br>
advice.<br>
Subsequently, i moved on with NPT and it stopped due to LINCS warning as<br>
below:-<br>
<br>
Step 269, time 0.538 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max inf (between atoms 1980 and 1981) rms inf<br>
bonds that rotated more than 30 degrees:<br>
<br>
This mean that some of the atoms in the structure is moving and it is out of<br>
the cutt-off which being defined, it also said that it might due to the<br>
reason that the starting structure is not equilibrated or many overlaps. But<br>
as what i know,<br>
the structure is well equilibrated. What is the reason for this? Is it<br>
something which i missed out during NVT or NPT? Please advice.<br>
<br>
<br>
Regards,<br>
Bing<br>
<br>
</blockquote>
<br>
<br></div></div>
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