[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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