Paymon Pirzadeh wrote:
I made a .tpr file for my md run without any problems (using the bottom
mdp file). My job submission script is also the same thing I used for
other jobs which had no problems. But now when I submit this .tpr file,
only an empty log file is generated! The qstat of the cluster shows that
the job is running, also the processors are 100% engaged while I have no
outputs!
Check that a short version of this job runs fine on a local machine.
Probably you are having some problem with a file system and/or its
buffering. Inspect your quotas. Talk to your system admins.
Mark
Here is my mdp file:
title = Yo
cpp = cpp
include = -I../top
define = -DPOSRES
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 3000000 ;3 ns
comm_mode = linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy = 5000
nstxtcout = 1500
nstvout = 5000
nstfout = 5000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist = 0.9
pbc = xyz
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
;epsilon_r = 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft = yes
; Temperature coupling
tcoupl = v-rescale
ld_seed = -1
tc-grps = System
tau_t = 0.1
ref_t = 275
; Pressure Coupling
Pcoupl = no
;Pcoupltype = isotropic
;tau_p = 1.0
;compressibility = 5.5e-5
;ref_p = 1.0
gen_vel = yes
gen_temp = 275
gen_seed = 173529
constraint-algorithm = Lincs
constraints = all-bonds
lincs-order = 4
I am not sure where things go wrong!
Payman
On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on
computers can be inexact, such that things like 0.02 added to itself 100
times does not pass a test for equality with 2. You may be observing
this kind of thing here. Your protein's [atoms] directive has a running
count of the total charge on the molecule - go and read it and see that
each residue has an integral charge. Hopefully you can observe where the
rounding error might be occurring and you can make a judgement about
whether this might be true.
Mark
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