Jones de Andrade wrote:
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?
So that explains it: g_energy uses the names of the energy terms, and
this exactly changed between 3.2 and 3.3. Hence Coul. Recip is not
recognized as an energy term by the old g_energy. By the way you have
rcoulomb > rlist, there you are using twin range cut-off. You probably
want to make them identical. Now you are computing the energies for
particles at distance between 1.25 and 1.30 only every nstlist steps,
while you are computing the energies for particles at Rij <= 1.25 and
particles at Rij>= 1.30 at every step.
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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.gromacs.org/mailman/listinfo/gmx-users
<http://www.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
