[gmx-users] NPT simulation for mutation study

[Shyno Mathew]

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)
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
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