AMBER Archive (2006)

Subject: Re: AMBER: Volume of ucell too big

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Sat Dec 16 2006 - 12:37:31 CST

Hi Atsutoshi,
I might be off base since I'm not an amber expert, but from your
previous email where you included your input file, I saw you set
constant pressure on, but didn't see you set an explicit pressure,
meaning the simulation defaults to 1.0 bar. Did you set a different
pressure. I haven't done any liquid methane simulations at ~ STP, but
isn't methane a gas at this state point which is going to expand in
volume (huge "ucell"?) I'm not sure the origin of the error (from
the volume changing too much for the grid approximations to hold?), but
my question about the physical simulation might be important.
Amber experts and physical chemistry experts, please correct me if I'm
way off!
-Nick

On Dec 16, 2006, at 12:41 AM, Atsutoshi Okabe wrote:

> Dear all,
>  
> I executed sander program to equilibrate the system in methane solvent
> box.
> But I got the following error message in output file.
>  
> NSTEP =    32400   TIME(PS) =      78.800  TEMP(K) =   296.90  PRESS
> =   116.7
>  Etot   =      3409.4640  EKtot   =      2349.6920  EPtot      =     
> 1059.7720
>  BOND   =        10.2431  ANGLE   =      1222.7808  DIHED     
> =        51.9193
>  1-4 NB =        10.1691  1-4 EEL =       140.2031  VDWAALS    =     
> -256.9207
>  EELEC  =      -137.2042  EHBOND  =         0.0000  RESTRAINT 
> =        18.5814
>  EAMBER (non-restraint)  =      1041.1905
>  EKCMT  =       628.4852  VIRIAL  =       149.0902  VOLUME     =   
> 190305.2399
>                                                    Density   
> =         0.1032
>  Ewald error estimate:   0.1011E-01
>  ----------------------------------------------------------------------
> --------
>  
>  SANDER BOMB in subroutine nonbond_list
>   volume of ucell too big, too many subcells
>   list grid memory needs to be reallocated, restart sander
>  
>  
>  
> I can’t understand why I got the error message.
> But actually, I got the following warning message in tleap.
> (Solvent has no box, so preparing by making box including vdw)
>  
> AMBER General Force Field for organic mol., add. info. at the end
> (June, 2003)
> > source tleap
> ----- Source: ./tleap
> ----- Source of ./tleap done
> Loading parameters: ./HEP.ff
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Loading Prep file: ./HEP.prep
> Loading parameters: ./TRE.ff
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Loading Prep file: ./TRE.prep
> Loading PDB file: ./CIS_HEP_TRE.pdb
>  (starting new molecule for chain B)
>   total atoms in file: 64
> Loading parameters: ./MET.ff
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Loading Prep file: ./MET.prep
> Loading PDB file: ./MET_HF_6-31g_opt.pdb
>   total atoms in file: 5
> Solvent has no box, so preparing by making box including vdw
> (Use 'setBox centers' first if box was pre-equilibrated)
>   Solute vdw bounding box:              12.168 12.838 11.434
>   Total bounding box for atom centers:  40.168 40.838 39.434
>   Solvent unit box:                     4.510 4.748 4.481
>   Total vdw box size:                   40.590 42.732 40.329 angstroms.
>   Volume: 69950.323 A^3
>   Total mass 11828.282 amu,  Density 0.281 g/cc
>   Added 710 residues.
>  
> Is its message caused the sander error message like above?
>  
> Could you please give me any suggestions to solve this problem?
>  
> Thank you
>  
> Atsutoshi

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