NG HUI WEN wrote:
Dear gmxusers,
I have a very basic question here which I hope someone could help me
with. I was running a couple of simulations over the weekend on a shared
cluster and both came to a stop for the same reasons:
Program mdrun_mpi, VERSION 4.0.7
Source code file: trnio.c, line: 252
File input/output error:
Cannot write trajectory frame; maybe you are out of quota?
Indeed there were quite a number of large files in my user
directory (e.g. the .trr files and etc). I think the problems probably
arise from the fact that (i) I am storing my trajectory as full
precision .trr files and (ii) setting too small a value for nstxout and
nstvout in .mdp.
I have seen some tutorials that suggested using "trjconv" to derive the
reduced precision .xtc files from the .trr files and then discard the
latter. My question is, would this be wise as I am not sure whether I
would find myself needing these .trr files in the future.
Then consider your objectives. Does your intended analysis require full
precision? Do you need the velocities? How many data points will you really
need? For the majority of analyses that one might perform, .xtc files suffice,
so you can skip the .trr file altogether and write an .xtc file using nstxtcout.
Also of interest:
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
Here's a snippet of my .mdp file. Am I saving my coordinates and
velocities too frequently? If I were to increase this, are there any
compelling factors that I need to take into considerations?
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
I really see no need for such output every 0.2 ps. I would consider 5000 data
points per ns overkill for most applications.
-Justin
Many thanks for your help!
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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