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)?
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 -- 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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