On 2012-04-16 17:23, Shyno Mathew wrote:
Dear Gromcas users,
I am doing some mutation study, NPT simulations. Initially I was using a
generic .mdp file I got from my advisor and I was able to run the
systems for ~50ns with out any issues.
But then I spend time reading about gromacs and created a .mdp file.
However, with my .mdp file the runs are crashing with error:
Fatal error:
The X-size of the box (4.500406) times the triclinic skew factor
(1.000000) is smaller than the number of DD cells (5) times the smallest
allowed cell size (0.900000)
use isotropic pressure scaling.
if you make mutations, take care to use the same number of water
molecules and ions, such that you can compare the energies of the systems.
I understand I can try particle decomposition for this system, but
before I want to make sure there is no error in my .mdp file.
When I load the trajectory in the vmd, I can see the box is getting
compressed too much. The contents of the current .mdp file are shown below.
This .mdp file varies from my advisor's for few parameters which I have
shown at the end.
contents of my .mdp file:
title = Yo
cpp = /usr/bin/cpp
include =
define =
integrator = sd
tinit = 0.0
dt = 0.002
nsteps = 50000000
nstxout = 1000000
nstvout = 1000000
nstfout = 1000000
nstlog = 10000
nstenergy = 10000
nstxtcout = 10000
xtc_precision = 1000
xtc_grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
domain-decomposition = no
coulombtype = PME
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
optimize_fft = no
epsilon_surface = 0
ewald_geometry = 3d
rcoulomb = 0.9
vdwtype = Cut-off
rvdw = 0.9
epsilon_r = 1
DispCorr = EnerPres
; with sd as integrator tcoupl is ignored
tc-grps = system
; good choice for zeta is 0.5 1/s
tau_t = 2.0
ref_t = 310
pcoupl = berendsen
pcoupltype = anisotropic
nstpcouple = -1
tau_p = 1.0
compressibility = 4.6e-5 4.6e-5 4.6e-5 0 0 0
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0
annealing = no
;annealing_npoints = 3
;annealing_time = 0
gen_vel = no
gen_temp = 310
gen_seed = 173529
constraints = all-bonds
constraint_algorithm = LINCS
continuation = no
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
morse = no
disre = no
disre_weighting = equal
disre_mixed = no
disre_fc = 1000
disre_tau = 10
nstdisreout = 1000
Parameters that are different in my advisor's file:
DispCorr = Ener
tau_t = 0.20
compressibility = 5e-6 5e-6 5e-6 0 0 0
gen_vel = yes
gen_temp = 1
gen_seed = 473529
I thought when using vdw cutoff, it is recommended to use dispersion
corrections for both pressure and energy. Also can some explain the
reason behind this?
For tau_t, I used 2 as it is the recommended value for sd integrator in
the manual. Also gen_vel has to be no for sd integrator, correct?
Any help will be appreciated!
Thanks in advance,
Shyno
--
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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