[gmx-users] intermolecular energy

[Jones de Andrade]

Hi David.

Well, as long as I can remember, I pushed the last gromacs sources at time (
3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and g_energy
says it is 3.2.1 (in the run headers). I expected this to be normal, or
could I have run in some kind of unnexpected or unremembered problem?

About coul.recip.: Those results above, of the big list, all include -nmol
500. It means that coul. recip. should be divided by 500² instead of only
500?

About twin-range: only if I'm unaware of it. In order to be sure, I'm
pasting here the mdp file I'm using. But, as far as I know, the answer is
no, I'm not using twin-range.

Tnaks a lot in advance,

Sincerally yours,

Jones

.mdp file follows:

cpp                 =  /lib/cpp
integrator          =  md
tinit               =   3650.000
dt                  =      0.002
nsteps              = 125000
nstcomm             =      1
nstxout             =      0
nstvout             =      0
nstfout             =      0
nstxtcout           =     10; 5  ;10
xtc-precision       =   1000 ;NAO MEXER!
nstlog              =     10
nstenergy           =     10
nstlist             =      5
energygrps          =  System
ns_type             =  grid

; Constraints use is:
constraints         =  none
constraint_algorithm = lincs

;Treatment of Vdw and Elctrostatics:
vdwtype             =  cut-off
DispCorr            =  EnerPres
rlist               =  1.25
rvdw                =  1.25
coulombtype         =  PME
rcoulomb            =  1.30
fourierspacing      =  0.1
pme_order           =  4
ewald_rtol          =  1e-05
optimize_fft        =  yes

; Temperature coupling is:
Tcoupl              =  nose-hoover
tau_t               =  0.030
tc-grps             =  System
ref_t               =  123.15

; Pressure coupling is:
Pcoupl              =  Parrinello-Rahman
pcoupltype          =  isotropic
tau_p               =  2.500
compressibility     =  4.5e-5
ref_p               =  1.01325 ;bar == 1. atm

; Generate velocites at 123K is:
gen_vel             =  no
gen_temp            =  123.15
;gen_seed            =  173529
gen_seed            =  12041979

On 6/23/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Hi all.
> >
> > First, I would like to apologize for the previous message. Maybe I've
> > been too "harsh"? Sorry for that.
> >
> > Second, I would like to list all the energetic contributions for one
> > (same system, different run) run that g_energy allowed me to get:
> >
> > Energy                      Average       RMSD     Fluct.      Drift
> > Tot-Drift
> >
> -------------------------------------------------------------------------------
> > Bond                        2.05116  0.0591887          0  - 0.123751
> > -30.9381
> > Angle                         2.638  0.0664036          0   0.114896
> > 28.7242
> > LJ (SR)                    -14.3726  0.0865671          0 -0.0877988
> > -21.9499
> > Disper. corr.             -0.378693 0.00211843          0 -0.00185533
> > -0.463837
> > Coulomb (SR)               0.128875  0.0164563          0 0.000956545
> > 0.239138
> > Coulomb (LR)             0.00237452 4.3944e-05          0 3.95014e-05
> > 0.00987542
> > Coul. recip.               - 145.145   0.660423   0.652976 -0.00137031
> > -0.34258
> > Potential                  -10.2211   0.138681          0 -0.0988822
> > -24.7207
> > Kinetic En.                 7.67642  0.0990863  0.0988019 0.000103943
> > 0.025986
> > Total Energy               -2.54473   0.167497          0 -0.0987789
> > -24.6949
> >
> > Temperature                  123.15     1.5896     1.5896 3.34002e-06
> > 0.000835011
> >
> Do you use an old version of g_energy with a newer mdrun?
>
> --
> 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://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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