Thanks Justin. The help has been much appreciated.
Cheers, Davide On 7/02/13 8:46 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 2/7/13 2:29 PM, Davide Mercadante wrote: >> Thank you Justin, >> >> I guess this means that this kind of simulations is not possible >>without a >> modification of the forcefield (which would ultimately mean using a >> different forcefield I believe)? >> > >If you're looking to unfold secondary structure elements, yes. > >-Justin > >> Thanks. >> >> Cheers, >> Davide >> >> On 7/02/13 8:09 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: >> >>> >>> >>> On 2/7/13 1:44 PM, Davide Mercadante wrote: >>>> Dear Justin, >>>> >>>> Thank you for your reply. I decreased the time step from 0.02 to 0.005 >>>> and >>>> run the simulation again. The simulation still crashes giving LINCS >>>> warning on the same atoms but does it later. >>>> Do you advice to keep reducing the time step in order to reach a >>>> simulated >>>> time where the pull of the whole molecule occurs and I see the force >>>> peaking? I am still not sure why this happens... >>>> >>> >>> No, I think the issue is probably more fundamental. MARTINI uses fixed >>> secondary structure (bonds in the topology to preserve geometry). >>>You're >>> probably just pulling against those and the algorithms that work on >>> bonded >>> interactions are failing. >>> >>> -Justin >>> >>>> Thanks. >>>> >>>> Davide >>>> >>>> On 7/02/13 1:05 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: >>>> >>>>> >>>>> >>>>> On 2/7/13 5:20 AM, Davide Mercadante wrote: >>>>>> Dear All, >>>>>> >>>>>> I am trying to run a pulling simulation on a small protein (18 aa) >>>>>> using >>>>>> the GC forcefield MARTINI (v2.2). I have energy minimized and >>>>>> equilibrated (NPT) my system and everything seems fine. My system >>>>>> consists of the protein + water + ions NA+ and CL-. >>>>>> >>>>>> After the equilibration I start a constant velocity pulling along >>>>>>the >>>>>> z-direction of the last atom of the chain while the first atom is >>>>>> positionally restrained in xyz (basically I am stretching the >>>>>> protein). >>>>>> At some point from the start of the pulling simulation and before >>>>>> reaching the full extension of the chain (force profile is still >>>>>> steadily increasing without peaking) the simulation crashes giving >>>>>>me >>>>>> these LINCS warnings: >>>>>> >>>>>> Step 293252, time 5865.04 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.157274, max 0.291135 (between atoms 10 and 11) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> >>>>>> Step 293252, time 5865.04 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.128562, max 0.230219 (between atoms 7 and 8) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> >>>>>> Step 293253, time 5865.06 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.413291, max 0.828515 (between atoms 7 and 8) >>>>>> >>>>>> Step 293253, time 5865.06 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.587032, max 0.986890 (between atoms 11 and 13) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 7 8 46.6 0.2686 0.0579 0.3500 >>>>>> 10 11 121.3 0.2481 0.0550 0.3500 >>>>>> 13 15 168.5 0.2851 0.0278 0.3500 >>>>>> >>>>>> Step 293253, time 5865.06 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.108373, max 0.322423 (between atoms 19 and 21) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 7 8 45.0 0.2686 0.0600 0.3500 >>>>>> 10 11 88.1 0.2481 0.0497 0.3500 >>>>>> Wrote pdb files with previous and current coordinates >>>>>> Wrote pdb files with previous and current coordinates >>>>>> >>>>>> Step 293254, time 5865.08 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.330732, max 0.654588 (between atoms 23 and 25) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 21 23 42.0 0.2905 0.1426 0.3500 >>>>>> 17 18 92.9 0.3146 0.1560 0.3000 >>>>>> 15 17 35.3 0.5839 0.4003 0.3500 >>>>>> 13 15 141.6 0.0278 0.2742 0.3500 >>>>>> >>>>>> Step 293254, time 5865.08 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.312540, max 0.555587 (between atoms 19 and 21) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 8 9 48.0 0.3406 0.1435 0.3100 >>>>>> 7 8 82.3 0.0579 0.4596 0.3500 >>>>>> 10 11 102.9 0.0550 0.5130 0.3500 >>>>>> 11 12 51.9 0.5425 0.3643 0.4000 >>>>>> 11 13 38.5 0.6954 0.1898 0.3500 >>>>>> 13 15 143.4 0.0278 0.2879 0.3500 >>>>>> 15 17 37.3 0.5839 0.3730 0.3500 >>>>>> >>>>>> Step 293254, time 5865.08 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.343084, max 0.751867 (between atoms 3 and 5) >>>>>> 17 18 93.2 0.3146 0.1563 0.3000 >>>>>> 21 23 41.6 0.2905 0.1443 0.3500 >>>>>> 23 24 33.0 0.3784 0.4007 0.4000 >>>>>> 11 13 58.2 0.6954 0.3283 0.3500 >>>>>> 23 24 33.1 0.3784 0.3999 0.4000 >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 7 8 82.2 0.0579 0.4605 0.3500 >>>>>> 8 9 48.4 0.3406 0.1439 0.3100 >>>>>> 10 11 104.0 0.0550 0.5496 0.3500 >>>>>> 11 12 57.6 0.5425 0.3679 0.4000 >>>>>> 11 13 61.9 0.6954 0.1402 0.3500 >>>>>> 13 15 141.2 0.0278 0.4588 0.3500 >>>>>> Wrote pdb files with previous and current coordinates >>>>>> Wrote pdb files with previous and current coordinates >>>>>> Wrote pdb files with previous and current coordinates >>>>>> >>>>>> Step 293255, time 5865.1 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 32.745333, max 105.228383 (between atoms 17 and 18) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 5 6 30.3 0.3950 0.3971 0.4000 >>>>>> 13 15 172.9 0.2879 4.6287 0.3500 >>>>>> 15 16 33.0 0.2435 5.0674 0.3300 >>>>>> 15 17 51.2 0.3730 11.1793 0.3500 >>>>>> 17 18 107.1 0.1563 31.8685 0.3000 >>>>>> 17 19 143.4 0.3380 10.1576 0.3500 >>>>>> 19 20 86.5 0.3397 6.2047 0.3300 >>>>>> 21 22 103.7 0.3750 6.6220 0.4000 >>>>>> 21 23 150.3 0.1426 6.8152 0.3500 >>>>>> >>>>>> Step 293255, time 5865.1 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 10.273318, max 30.025748 (between atoms 19 and 21) >>>>>> 23 24 149.4 0.3999 1.3487 0.4000 >>>>>> 25 26 79.9 0.3039 2.4910 0.3000 >>>>>> 25 27 165.9 0.2225 2.4307 0.3500 >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 21 22 103.7 0.3750 6.6180 0.4000 >>>>>> 21 23 150.2 0.1426 6.8083 0.3500 >>>>>> 19 20 86.5 0.3397 6.2048 0.3300 >>>>>> 17 19 143.4 0.3380 10.1586 0.3500 >>>>>> 17 18 107.1 0.1563 31.8685 0.3000 >>>>>> 15 17 51.2 0.3730 11.1771 0.3500 >>>>>> 15 16 33.0 0.2435 5.0657 0.3300 >>>>>> 13 15 173.1 0.2879 4.6383 0.3500 >>>>>> 23 24 149.5 0.3999 1.3474 0.4000 >>>>>> 25 26 79.9 0.3039 2.4804 0.3000 >>>>>> 25 27 165.7 0.2225 2.3691 0.3500 >>>>>> 28 29 44.1 0.3191 0.0921 0.3100 >>>>>> 28 30 39.4 0.3101 0.2122 0.3500 >>>>>> Wrote pdb files with previous and current coordinates >>>>>> Wrote pdb files with previous and current coordinates >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256 Warning: pressure scaling more than 1%, mu: 2.21304 >>>>>> 2.21304 >>>>>> 2.21304 >>>>>> >>>>>> Step 293256, time 5865.12 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 3192.715629, max 6000.654094 (between atoms 25 and 26) >>>>>> >>>>>> Step 293256, time 5865.12 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 0.212149, max 0.517573 (between atoms 5 and 7) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 5 7 37.9 0.3543 0.5312 0.3500 >>>>>> 7 8 33.5 0.3821 0.3834 0.3500 >>>>>> 8 9 56.8 0.3361 0.3502 0.3100 >>>>>> 8 10 165.7 0.3548 1.0526 0.3500 >>>>>> >>>>>> Step 293256, time 5865.12 (ps) LINCS WARNING >>>>>> relative constraint deviation after LINCS: >>>>>> rms 95.799929, max 246.403254 (between atoms 19 and 21) >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 8 9 56.7 0.3361 0.3566 0.3100 >>>>>> 8 10 165.7 0.3548 1.0708 0.3500 >>>>>> 7 8 33.4 0.3821 0.3897 0.3500 >>>>>> 5 7 37.9 0.3543 0.5312 0.3500 >>>>>> 11 12 121.6 0.2312 2.6433 0.4000 >>>>>> 11 13 149.8 0.3060 15.6610 0.3500 >>>>>> 13 14 123.6 0.4129 14.6116 0.4000 >>>>>> 13 14 124.2 0.4129 14.9085 0.4000 >>>>>> 13 15 169.6 4.6287 44.1184 0.3500 >>>>>> 11 12 121.1 0.2312 2.7328 0.4000 >>>>>> 11 13 149.6 0.3060 15.9678 0.3500 >>>>>> 15 16 168.1 5.0674 39.6694 0.3300 >>>>>> 15 17 159.6 11.1793 63.3062 0.3500 >>>>>> 17 18 114.1 31.8685 33.0371 0.3000 >>>>>> 17 19 112.0 10.1576 36.5026 0.3500 >>>>>> 19 20 71.0 6.2047 9.2619 0.3300 >>>>>> 23 24 62.3 1.3474 352.2061 0.4000 >>>>>> 25 26 63.9 2.4804 1800.5086 0.3000 >>>>>> 25 27 67.1 2.3691 2007.2339 0.3500 >>>>>> 13 15 169.4 4.6287 43.0156 0.3500 >>>>>> 27 28 66.0 0.6878 1992.3756 0.3500 >>>>>> bonds that rotated more than 30 degrees: >>>>>> atom 1 atom 2 angle previous, current, constraint length >>>>>> 19 20 71.0 6.2047 9.2610 0.3300 >>>>>> 17 19 112.0 10.1576 36.4983 0.3500 >>>>>> 17 18 114.1 31.8685 33.0303 0.3000 >>>>>> 15 17 159.6 11.1793 63.3215 0.3500 >>>>>> 15 16 168.1 5.0674 39.6801 0.3300 >>>>>> 13 15 169.6 4.6287 44.0779 0.3500 >>>>>> 13 14 124.6 0.4129 14.7983 0.4000 >>>>>> 11 13 148.8 0.3060 16.1472 0.3500 >>>>>> 23 24 62.3 1.3474 352.1905 0.4000 >>>>>> 25 26 63.9 2.4804 1800.4962 0.3000 >>>>>> 25 27 67.1 2.3691 2007.1944 0.3500 >>>>>> 27 28 66.0 0.6878 1992.3052 0.3500 >>>>>> 28 29 44.6 0.0921 600.7400 0.3100 >>>>>> 28 30 137.0 0.2122 696.2760 0.3500 >>>>>> 30 31 38.7 0.2803 155.6825 0.2650 >>>>>> Wrote pdb files with previous and current coordinates >>>>>> Wrote pdb files with previous and current coordinates >>>>>> >>>>>> I have a feeling that this happens when I am reaching the full >>>>>> extension >>>>>> of the chain because if in the input file (pull.mdp - copied below) >>>>>>I >>>>>> increase the pull rate the simulation simply crashes before. >>>>>> This crash does not happen in a full-atom simulation of the same >>>>>> protein >>>>>> (using for example OPLS) and the force profile reaches the peak >>>>>>wanted >>>>>> when the protein approaches the full extension. >>>>>> >>>>>> I was wondering if you please could help me to understand why this >>>>>> happens, if this is a force-field related issue and how I could >>>>>> possibly >>>>>> solve the problem. >>>>>> The force costant I apply in the posre.itp file for atom number 1 is >>>>>> 5000 kj mol^1 nm^2 while the pulling force constant (harmonic >>>>>> potential) >>>>>> is 500 kj mol^1 nm^2. >>>>>> The pull.mdp input file is appended below. >>>>>> >>>>>> title = Umbrella pulling simulation >>>>>> define = -DPOSRES >>>>>> ; Run parameters >>>>>> integrator = md >>>>>> dt = 0.02 >>>>>> tinit = 0 >>>>>> nsteps = 500000 ; 10000.00 ps >>>>>> nstcomm = 10 >>>>>> ; Output parameters >>>>>> nstxout = 100 ; every 2 ps >>>>>> nstvout = 100 >>>>>> nstfout = 100 >>>>>> nstxtcout = 100 ; every 2 ps >>>>>> nstenergy = 100 >>>>>> ; Bond parameters >>>>>> constraint_algorithm = lincs >>>>>> constraints = all-bonds >>>>>> continuation = yes ; continuing from NPT >>>>>> ; Single-range cutoff scheme >>>>>> nstlist = 5 >>>>>> ns_type = grid >>>>>> rlist = 1.4 >>>>>> rcoulomb = 1.4 >>>>>> rvdw = 1.4 >>>>>> ; PME electrostatics parameters >>>>>> coulombtype = PME >>>>>> fourierspacing = 0.12 >>>>>> fourier_nx = 0 >>>>>> fourier_ny = 0 >>>>>> fourier_nz = 0 >>>>>> pme_order = 4 >>>>>> ewald_rtol = 1e-5 >>>>>> optimize_fft = yes >>>>>> ; Berendsen temperature coupling is on in two groups >>>>>> Tcoupl = V-rescale >>>>>> tc_grps = Protein Non-Protein >>>>>> tau_t = 2 2 >>>>>> ref_t = 310 310 >>>>>> ; Pressure coupling is on >>>>>> Pcoupl = Berendsen >>>>>> pcoupltype = isotropic >>>>>> tau_p = 2.0 >>>>>> compressibility = 4.5e-5 >>>>>> ref_p = 1.0 >>>>>> refcoord_scaling = com >>>>>> ; Generate velocities is off >>>>>> gen_vel = no >>>>>> ; Periodic boundary conditions are on in all directions >>>>>> pbc = xyz >>>>>> ; Long-range dispersion correction >>>>>> DispCorr = EnerPres >>>>>> >>>>>> ; PULL-CODE >>>>>> >>>>>> pull = umbrella >>>>>> pull_geometry = direction >>>>>> pull_start = yes ; (we don't want to calculate the initial distance >>>>>> between 'pull' and 'freeze' by hand) >>>>>> pull_ngroups = 1 ; (because the reference group doesn't count to >>>>>>this >>>>>> value) >>>>>> pull_dim = N N Y ; (because we want to pull only along the z-axis) >>>>>> pull_group0 = freeze >>>>>> pull_group1 = pull >>>>>> pull_vec1 = 0 0 1 >>>>>> pull_init1 = 0.0 0.0 0.0 >>>>>> pull_rate1 = 0.001 >>>>>> pull_k1 = 500 >>>>>> pull_constr_tol = 1e-6 >>>>>> pull_pbc_atom0 = 0 >>>>>> pull_kB1 = 500 >>>>>> pull_nstxout = 100 ; every 2 ps >>>>>> pull_nstfout = 100 ; every 2 ps >>>>>> >>>>>> Thank you, any suggestions will be greatly appreciated. >>>>> >>>>> Try reducing the time step. >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Research Scientist >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>> >>>>> ======================================== >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >-- >======================================== > >Justin A. Lemkul, Ph.D. >Research Scientist >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? 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