[gmx-users] RNA and water

[David]

On Fri, 2005-11-04 at 00:32 +0100, vincenzo venditti wrote:
> Dear all,
> i have a problem concerning a MD simulation on a small RNA structure.
> I have minimized the structure in vacum reaching the following result:
>  
>            Step           Time         Lambda
>             627      627.00000        0.00000
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.
> LJ-14
>     2.45163e+02    6.40761e+02    3.78574e+00    1.76619e+03
> 7.44530e+02
>      Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
> Potential
>    -1.23051e+04   -1.46899e+03   -1.82476e+03    3.01441e+03
> -9.18396e+03
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00
>  
> The structure semms pretty good, but when I add water (ffamber_tip4p)
> to run the energy minimization in the solvent box the LJ (SR) shows to
> very high values also at the end of minimization:
>  
> 
>            Step           Time         Lambda
>               0        0.00000        0.00000
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.
> LJ-14
>     2.67813e+02    6.44749e+02    3.98629e+00    1.76818e+03
> 7.42894e+02
>      Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
> Potential
>    -1.23031e+04    6.22337e+04   -2.70809e+05   -3.59886e+04
> -2.53439e+05
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00
>  
>  
>  
>           Step           Time         Lambda
>            2031     2031.00000        0.00000
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.
> LJ-14
>     2.62036e+02    7.38608e+02    9.55040e+00    1.74683e+03
> 7.08018e+02
>      Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
> Potential
>    -1.23454e+04    5.91634e+04   -3.68597e+05   -4.18478e+04
> -3.60162e+05
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00 
>  
> Then, if I try to run a position restrain or a simulated annealing on
> the minimized sistem I observe a very high pressure value and sistem
> crush after few iterations.
> What could I do?
> Do you think that to lower the system density, to increase the box
> size or change water topology (ffamber_tip3p) may be good way to
> overcome the problem?

Water always has a positive LJ, to compensate for the strong Coulomb
interactions. For SPC it is roughly a ratio of -5 (Coulomb / LJ) which
is roughly what you have here too.

I suggest you start with position restraints on your RNA, and no
pressure coupling. The you run with posres and P coupling, then finally
without posres.


> Bests,
> Vincenzo
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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