[gmx-users] Re: LINCS WARNING relative constraint deviation
E. Nihal Korkmaz
enihalkorkmaz at gmail.com
Mon Jun 20 18:10:26 CEST 2011
What would you suggest as a short time step? I was using 0.002 ps. And just
to make sure, would 5 ns of equilibration be enough for a ~110 amino acid
long protein?
Thanks,
Nihal
On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham <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> 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
>> Email: 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
> Email: 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
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