[gmx-users] MARTINI force-field in pulling simulations
Davide Mercadante
dmer018 at aucklanduni.ac.nz
Fri Feb 8 17:45:11 CET 2013
Thanks Justin.
The help has been much appreciated.
Cheers,
Davide
On 7/02/13 8:46 PM, "Justin Lemkul" <jalemkul at 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" <jalemkul at 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" <jalemkul at 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 at gromacs.org
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>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> 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 at gromacs.org
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>>
>>
>
>--
>========================================
>
>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
>
>========================================
>--
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