[gmx-users] Re: LINCS WARNING relative constraint deviation
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Jun 20 19:48:54 CEST 2011
On 21/06/2011 2:10 AM, E. Nihal Korkmaz wrote:
> What would you suggest as a short time step? I was using 0.002 ps.
I'd suggest starting with maybe 100ps of 0.0005 ps time steps, but
that's probably overkill.
> And just to make sure, would 5 ns of equilibration be enough for a
> ~110 amino acid long protein?
I guess so. It's cheap.
Mark
> Thanks,
> Nihal
>
> On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
>> I also checked the output of the minimization:
>>
>> Steepest Descents converged to machine precision in 402 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy = -1.81875038188621e+04
>> Maximum force = 3.20769543152855e+02 on atom 331
>> Norm of force = 2.04356801849931e+01
>>
>> I assume the structure is not relaxed enough to start a
>> simulation. How can I get it minimize further? I increased the
>> step size up to 0.1 ps, i still get the same result.
>
> The minimization is probably OK, but a period of equilibration at
> a short time step will probably help smooth the process out.
> Simulations in implicit solvent have few explicit degrees of
> freedom compared to explicit solvent, and might be rather more
> susceptible to equilibration issues if the generated velocities
> are randomly not-quite-good-enough.
>
> Mark
>
>
>> Thanks,
>> Nihal
>>
>> On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz
>> <enihalkorkmaz at gmail.com <mailto:enihalkorkmaz at gmail.com>> wrote:
>>
>> Dear all,
>>
>> I am trying to simulate a GB simulation of a 112 amino acid
>> long protein. I keep getting these errors,
>>
>> Step 27718, time 55.436 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 33.319842, max 438.763717 (between atoms 79 and 81)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>>
>> Step 27718, time 55.436 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.058237, max 1.390675 (between atoms 91 and 93)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 91 92 50.2 0.1016 0.1065 0.1010
>> 91 93 90.0 0.1002 0.2415 0.1010
>> 91 94 70.2 0.1025 0.1066 0.1010
>> 79 80 90.0 0.1057 1.0667 0.1090
>> 79 81 90.0 1.3066 47.9342 0.1090
>> 85 86 90.0 0.1084 0.1758 0.1090
>> 85 87 90.0 1.0654 0.1668 0.1090
>> 88 89 90.0 0.1097 0.6994 0.1090
>> 88 90 90.0 0.1125 0.1097 0.1090
>> 91 92 50.2 0.1016 0.1065 0.1010
>> 91 93 90.0 0.1002 0.2415 0.1010
>> 91 94 70.2 0.1025 0.1066 0.1010
>>
>>
>> I am copying my mdp parameters below, I'd appreciate any
>> suggestions to fix that.
>>
>> integrator = sd
>> tinit = 0
>> dt = 0.002
>> nsteps = 2500000
>> simulation_part = 1
>> init_step = 1
>>
>> nstxout = 5000
>> nstvout = 5000
>> nstenergy = 500
>> nstxtcout = 500
>> nstlog = 500
>>
>> xtc_grps = System
>> energygrps = System
>> comm_mode = Linear
>> ; neighbor searching and vdw/pme setting up
>> nstlist = 10
>> ns_type = grid
>> pbc = xyz
>> rlist = 2.0
>>
>> implicit_solvent = GBSA
>> gb_algorithm = OBC
>> gb_saltconc = 0.15
>> rgbradii = 2.0
>>
>> coulombtype = Cut-off
>> fourierspacing = 0.1
>> pme_order = 6
>> rcoulomb = 2.0
>>
>> vdwtype = Cut-off
>> rvdw_switch = 1.0
>> rvdw = 2.0
>>
>> ; cpt control
>> tcoupl = V-rescale
>> tc-grps = System
>> tau_t = 0.1
>> ref_t = 300.0
>>
>> Pcoupl = Berendsen
>> pcoupltype = isotropic
>> tau_p = 1.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>>
>> ; velocity & temperature control
>> gen_vel = yes
>> gen_temp = 300.0
>> annealing = no
>> constraints = hbonds
>> constraint_algorithm = lincs
>> morse = no
>>
>>
>> Thanks,
>> --
>> Elif Nihal Korkmaz
>>
>> Research Assistant
>> University of Wisconsin - Biophysics
>> Member of Qiang Cui & Thomas Record Labs
>> 1101 University Ave, Rm. 8359
>> Madison, WI 53706
>> Phone: 608-265-3644 <tel:608-265-3644>
>> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>>
>>
>>
>>
>>
>> --
>> Elif Nihal Korkmaz
>>
>> Research Assistant
>> University of Wisconsin - Biophysics
>> Member of Qiang Cui & Thomas Record Labs
>> 1101 University Ave, Rm. 8359
>> Madison, WI 53706
>> Phone: 608-265-3644 <tel:608-265-3644>
>> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>>
>>
>
>
> --
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>
>
>
> --
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone: 608-265-3644
> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>
>
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