[gmx-users] Energy Minimization of DNA

[Justin A. Lemkul]

David Crosby wrote:
> Hello all, how are you doing today?
> 
> I've been trying to get a stable DNA MD simulation to work for me, but I
> think my problem lies in an insufficiently energy minimized system prior to
> running the pr step.  I'm using the ffamber99 force field and I've
> successfully simulated many ns of MD using the sample Dickerson dodecamer
> pdb file supplied on the gromacs web site.  However, when I build my own
> 21mer using NAB (http://casegroup.rutgers.edu/nab.html), I always get LINCS
> warnings during the first thousand steps of pr...  Here are my settings for
> em:
> 
> define = -DFLEXIBLE
> constraints = none
> integrator = steep
> dt = 0.001 ; ps !
> nsteps = 4000
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.08
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 8
> ewald_rtol = 1e-5
> optimize_fft = yes
> ;
> ; Energy minimizing stuff
> ;
> emtol = 10000.0
> emstep = 0.01
> 
> here's a sample of the em output: (27 steps sounds awfully short...)
> 
> Steepest Descents converged to Fmax < 10000 in 27 steps 
> Potential Energy  = -3.4305819e+05
> Maximum force     =  5.8583452e+03 on atom 495
> Norm of force     =  3.0654459e+02

Try for a lower force.  A value of 5000 is very large, and probably leads to the 
crash you see during position restrained equilibration.  Setting emtol to 1000 
or less is generally more appropriate.

-Justin

> And here are my settings for pr:
> 
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 20000 ; total 20.0 ps.
> nstcomm = 1
> nstxout = 250 ; collect data every 0.5 ps
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.08
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 8
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on
> Tcoupl = v-rescale
> tau_t = 0.1 0.1
> tc-grps = protein non-protein
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = parrinello-rahman
> Pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 310 K.
> gen_vel = yes
> gen_temp = 310.0
> gen_seed = 173529
> 
> and here's the output from the failed pr after about 500 steps:
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.5
> Source code file: constr.c, line: 136
> 
> Fatal error:
> Too many LINCS warnings (1000)
> If you know what you are doing you can adjust the lincs warning threshold in
> you
> r mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> -------------------------------------------------------
> 
> Thanks again for all your help! You folks are lifesavers!  All suggestions
> are welcome!
> 
> Dave Crosby
> UC Irvine, dept of pathology and laboratory medicine
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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