[gmx-users] pressure scaling more than 1%

[Wang Qin]

The system is a protein binding with one ligand and the ligand mutates to
another one. The problem is found when lamda=1. First of all I run a energy
minimization using an initial structure from the product of lamda=0.9. Then
the problem happens when I run a equilibrium.
Here is the mdp option:
cpp                      =/usr/bin/cpp
integrator               =
md

tinit                    = 0
dt                       = 0.002
nsteps                   = 50000
nstcomm                  = 1
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 500
nstenergy                =
100

nstxtcout                = 5000
xtc-precision            = 1000
nstlist                  = 1
ns_type                  = grid


Pcoupl                   = berendsen
tau_p                    = 1.0
compressibility          = 4.5e-05
ref_p                    = 1.0


tcoupl                   = nose-hoover
tc_grps                  = system
tau_t                    = 0.1
ref_t                    = 300

constraints              = none
constraint-algorithm     =
lincs

shake-tol                = 0.0001
lincs-order              = 12
lincs-warnangle          =
30

coulombtype              =
pme

rcoulomb                 = 1.0

epsilon-r                =
1

vdw-type                 =
switch

rvdw-switch              = 1.0
rvdw                     = 1.3
DispCorr                  =
EnerPres

fourierspacing           = 0.08

fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0


pme_order                = 6
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = yes


free_energy              = yes
init_lambda              = 1.0
delta_lambda             = 0
sc_alpha                 =0.5
sc-power                 =1.0
sc-sigma                 = 0.3


Thanks.


On 8/8/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> Wang Qin wrote:
> > Dear all,
> >           I am trying to do a FEP. In the equilibrium step, it fails
> > after about 500 steps with a warnning:  pressure scaling more than 1%,
> > mu: 1.06718 1.06718 1.06718. I searched the old discussion about it and
> > then try to increase the tau_p to 2 till 10. But it just goes futher but
> > still meets the problem at the end.
> >           Any idea about it?
>
> Not unless you tell us how you prepared this system. Almost certainly
> the initial structure is too far from the constant-P equilibrium state.
> Follow the kind of things that the tutorial material does, and also
> check out this link
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
>
> Mark
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