[gmx-users] MARTINI force-field in pulling simulations
Justin Lemkul
jalemkul at vt.edu
Thu Feb 7 20:46:28 CET 2013
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
>>>>
>>>> ========================================
>>>> --
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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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
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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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