[gmx-users] box explodes when using PME

[David]

On Tue, 2002-09-10 at 23:01, Attila Borics wrote:
> Hi,
> 
> My simulation crashed several times. As I checked everything it 
> turned out it has 2 possible causes.
> One is this message from flog: 
> 
> **************************************************************************
> 
>            Step           Time         Lambda      Annealing
>          138000      276.00000        0.00000        1.00000
> 
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.009921     29     30   0.002540
>         After LINCS         0.000026     20     22   0.000011
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14    
> Coulomb-14
>     5.65977e+01    4.01335e+01    1.56962e+01    1.10161e+01   
> 7.09566e+00
>         LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic
> En.
>    -1.74165e+02   -4.26500e+00   -6.57856e+03   -6.62645e+03   
> 1.12548e+04
>    Total Energy    Temperature Pressure (bar)
>     4.62831e+03    2.99177e+02    4.60669e+01
> 
> Grid: 28 x 28 x 28 cells
> WARNING: your box is exploding! (ncells = 21952)
> 
> *************************************************************************
> 
> Now I run this job on only 1 processor instead of a 4 membered ring and
> it seems to be OK (I mean it keeps running), but there`s definitely 
> something wrong with this: I keep getting this previous error message
> in flog.
> 
> Here`s my .mdp, Is there anything I`m doing wrong?
> 
> ;	User aborics
> ;	Thu 1/31/02
> ;	Input file
> ;
> title               =  DDKG
> warnings            =  10
> cpp                 =  /lib/cpp
> constraints         =  all-bonds
> constraint_algorithm     = Lincs
> integrator          =  md
> tinit               =  0.0
> dt                  =  0.002	; ps !
> nsteps              =  12550000	; total 25.1 ns
> nstcomm             =  1
> ; output
> nstxout		    =  1000
> nstxtcout           =  0
> nstvout             =  2000
> nstfout             =  5000
> nstlog		    =  1000
> nstenergy           =  1000
> ;
> nstlist             =  10
> ns_type             =  grid
> deltagrid           =  2
> ; eeltype	  
> rlist               = 0.9
> coulombtype         = PME
> epsilon_r	    = 78
This is probably it: you want to set this to one, as now your Coulomb
attraction is almost zero. For PME you can set epsilon_surface. You do
need a recent version of gromacs for this to work (>= 3.1 IIRC)

> rcoulomb            = 0.9
> vdwtype	            = cut-off
> rvdw                = 0.9
> fourierspacing      = 0.12
> pme_order           = 4
> ewald_rtol          = 1e-5
> ; box type
> pbc                   = xyz
> ; Temperature coupling is on in two groups
> Tcoupl              =  Berendsen
> tc-grps		    =  Protein	SOL  NA+  CL-
> tau_t               =  0.1	0.1  0.1  0.1
> ref_t               =  300	300  300  300
> ; Energy monitoring
> energygrps          =  Protein  SOL
> ; Pressure coupling
> Pcoupl              =  Berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> 
> Please, help.
> 
> Thanks
> 
> Attila
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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