[gmx-users] gcc problem
余翔
yux at iccas.ac.cn
Mon Nov 5 08:49:11 CET 2007
Dear all:
I have a problem when I was running mdrun on different computers. I made a .tpr file including coordinate and velocity of each atom from a crash of mdrun and upload it to four computers whose distribution version of linux and gcc were as follows:
computer A: Redhat 9.0, gcc 3.2.2
computer B: Turbo Linux 10,gcc 3.4.3
computer C: Redhat 7.2, gcc 2.96
computer D: Fedora core 6, gcc 3.4.6(the default version is 4.1.1, so I reinstalled an old version on it)
All the gmx are compiled in float and mpi mode.
The results of mdrun (the final .gro file, the trajectory file and the energy file) that start from the same .tpr file obtained on these computers are totally different, but if I ran mdrun on one computer from this .tpr file twice or more times, the results are all the same. So I don't know why the "mdrun" compiled by different versions of gcc would give such different results and which result should I trust. Does anybody know why it happens? I beg for your help...
this is the content of my .mdp file, I have modified nstlist, ns_type, pbc, rlist, rvdw and rcoulomb for many times, but it does not work.
title =
cpp = /usr/bin/cpp
include =
define = -DFLEXIBLE
integrator = md
tinit = 0
dt = 0.002
nsteps = 12000
init_step = 0
comm-mode = Angular
nstcomm = 1
comm-grps =
bd-fric = 0
ld-seed = 1993
emtol = 100
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
nstxout = 100
nstvout = 1000
nstfout = 0
nstcheckpoint = 1000
nstlog = 1000
nstenergy = 100
nstxtcout = 0
xtc-precision = 1000
xtc-grps =
energygrps =
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 0.9
domain-decomposition = no
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon_r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 0.9
DispCorr = No
table-extension = 1
energygrp_table =
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
Tcoupl = nose-hoover
tc-grps = System
tau-t = 0.1
ref-t = 600
Pcoupl = no
Pcoupltype = Isotropic
tau-p = 1
compressibility =
ref-p =
andersen_seed = 815131
QMMM = no
QMMM-grps =
QMmethod =
QMMMscheme = normal
QMbasis =
QMcharge =
QMmult =
SH =
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
MMChargeScaleFactor = 1
bOPT =
bTS =
annealing = no
annealing_npoints = 11
annealing_time =
annealing_temp =
gen_vel = no
gen-temp = 600
gen-seed = 173529
constraints = none
constraint-algorithm = Lincs
unconstrained-start = no
Shake-SOR = no
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
energygrp_excl =
disre = No
disre-weighting = Conservative
disre-mixed = no
disre-fc = 1000
disre-tau = 0
nstdisreout = 100
orire = no
orire-fc = 0
orire-tau = 0
orire-fitgrp =
nstorireout = 100
dihre = No
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
YuXiang
yux at iccas.ac.cn
2007-11-05
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