[gmx-users] ffamber port and RNA
Maik Goette
mgoette at mpi-bpc.mpg.de
Thu Nov 3 10:03:27 CET 2005
I fear, I can't help you that much, but I also got lincs warnings, when
working on DNA...
I solved the problem by choosing shake...;)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
sara pistolesi wrote:
> Dear all,
> I'm tryng to carry out a MD simulation on a small RNA fragment using
> ffamber94 in gromacs 3.3.1.
> I've modified my PDB file (as described at the web page
> http://folding.stanford.edu/ffamber/) and converted it in Gormacs format
> using pdb2gmx. Then I've solvated my system using editconf (cubic) and
> genbox (ffamber_tip4p) commads. To neutralize system charge I've added
> 21 Na+ using genion command. I've minimized the resulting system using
> the following mdp file.
>
> define = -DFLEX_SPC
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 10000
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ;
> ; Energy minimizing stuff
> ;
> emtol = 100.0
> emstep = 0.1
>
> The minimization was converged after 740 steps and the generated
> structure look pretty good.
> Starting from this structure, to equilibrate solvent, I 've tryed to run
> a position restrain using the following parameters:
>
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 10000 ; total 20.0 ps.
> nstcomm = 1
> nstxout = 250
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tc-grps = Protein SOL Na+
> tau_t = 0.1 0.1 0.1
> ref_t = 300 300 300
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
> During the grompp I've obtained the following WARNING message for the
> lines 426, 428, 429, 432 and 441:
>
> /usr/local/gromacs/share/gromacs/topffamber94bon.itp:426:22: warning:
> ISO C reqires whitespace after the macro name
>
> This message refer to the * position in these lines of ffamber94bon.itp
> file:
>
> ; missing nucleic torsions
> #define proper_X_CT_N*_X 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000
> #define proper_X_CM_CT_X 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000
> #define proper_X_CK_N*_X 14.22560 0.00000 -14.22560
> 0.00000 0.00000 0.00000
> #define proper_X_CB_N*_X 13.80720 0.00000 -13.80720
> 0.00000 0.00000 0.00000
> #define proper_X_CA_NC_X 40.16640 0.00000 -40.16640
> 0.00000 0.00000 0.00000
> #define proper_X_CQ_NC_X 56.90240 0.00000 -56.90240
> 0.00000 0.00000 0.00000
> #define proper_X_C_N*_X 12.13360 0.00000 -12.13360
> 0.00000 0.00000 0.00000
> #define proper_X_CM_CM_X 55.64720 0.00000 -55.64720
> 0.00000 0.00000 0.00000
> #define proper_X_C_NC_X 33.47200 0.00000 -33.47200
> 0.00000 0.00000 0.00000
> #define proper_X_CA_CM_X 21.33840 0.00000 -21.33840
> 0.00000 0.00000 0.00000
> #define proper_X_C_NA_X 11.29680 0.00000 -11.29680
> 0.00000 0.00000 0.00000
> #define proper_X_CA_NA_X 12.55200 0.00000 -12.55200
> 0.00000 0.00000 0.00000
> #define proper_X_CK_NB_X 83.68000 0.00000 -83.68000
> 0.00000 0.00000 0.00000
> #define proper_X_C_CM_X 18.20040 0.00000 -18.20040
> 0.00000 0.00000 0.00000
> #define proper_X_CA_N2_X 20.08320 0.00000 -20.08320
> 0.00000 0.00000 0.00000
> #define proper_X_N*_CM_X 15.48080 0.00000 -15.48080
> 0.00000 0.00000 0.00000
>
> What I have to do?
> Ignoring the warning, position restrain give the following warning :
>
> Step 6, time 0.012 (ps) LINCS WARNING
> relative costraint deviation after LINCS:
> max 0.001535 (between atoms 85 and 86) RMS 0.000106
> bond that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 565 566 33.3 0.1010 0.1010 0.1010
> .
> .
> and so on.
>
> Looking at the structures in trajectory file it is possible observe a
> total distortion of RNA structure.
> Then to overcome the problem I've tried to run a simulated annealing
> taking the RNA fixed:
>
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; 1000 ps !
> nsteps = 500000
> nstcomm = 1
> nstxout = 500
> nstvout = 500
> nstfout = 0
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in three groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1 0.1
> tc-grps = protein SOL Na+
> ref_t = 0 300 300
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 0
> annealing = single single single
> annealing_npoints = 2 11 11
> annealing_time = 0 1000 0 50 100 150 200 250 300 350 400 450
> 500 0 50 100 150 200 250 300 350 400 450 500
> annealing_temp = 0 0 0 30 60 90 120 150 180 210 240 270
> 300 0 30 60 90 120 150 180 210 240 270 300
>
> The results are almost the same.
> How can I do to equilibrate and simulate my system?
>
> I am sorry for the length of my post.
> Thanks in advance for all suggestions.
>
> Sara Pistolesi
>
>
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