The segmentation fault is highly unusual, and suggests that the
installation of gromacs used a shared library that has now
migrated/changed/whatever. I suggest you discuss that with your system
admins and ask them to re-install, or re-run the GROMACS regression tests,
to check things are OK.
Mark
On Mon, Mar 24, 2014 at 2:13 PM, Ankita Naithani
ankitanaith...@gmail.comwrote:
Hi Justin,
Thank you very much for your reply. I shall try to work my way around and
see.
Kind regards,
Ankita
On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/24/14, 7:57 AM, Ankita Naithani wrote:
Hi, so I modified my mdp file which now looks like the following:
title= production MD
; Run parameters
integrator= md; leap-frog algorithm
;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns
;nsteps= 20; 0.005 * 20 = 1 ns
;dt= 0.005; 5 fs
nsteps= ; 0.003 * = 10 ps or 100 n
dt= 0.003; 3 fs
; Output control
nstxout= 0; save coordinates every 2 ps
nstvout= 0; save velocities every 2 ps
nstxtcout= 1000; xtc compressed trajectory output every 5 ps
nstenergy= 1000; save energies every 5 ps
nstlog= 1000; update log file every 5 ps
; Bond parameters
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 25 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
rlistlong= 1.0; long-range neighborlist cutoff (in nm)
cutoff-scheme = Verlet
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
nstcomm = 10; remove com every 10 steps
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 318 318; reference temperature, one for each
group,
in K
; Pressure coupling is off
pcoupl = berendsen; Berendsen thermostat
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 1.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= yes; Velocity generation is on
gen_temp= 318; reference temperature, for protein in K
--
But, when I try to generate the tpr file on the cluster itself using
gromacs 4.6.3, I get the following error:
NOTE 1 [file md3.mdp]:
With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
NOTE 2 [file md3.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 3403 of the 3403 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3403 of the 3403 1-4 parameter combinations
Segmentation fault
Can anyone please suggest further?
Do as the notes suggest. They're not fatal errors, they're just
cautionary. You should probably educate yourself a bit further on what
all
of these algorithms are by taking a look at http://www.gromacs.org/
Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but
it is required by the type of parallelization you requested.
Reviewers may question the changes in version and cutoff methods when
critiquing your work, so be aware of that. Also, the instability you are
seeing is probably a result of the large time step, unless you are using
virtual sites.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu
