[gmx-users] cant load trajectory, low memory
abhisek Mondal
abhisek.mndl at gmail.com
Wed Apr 26 08:29:22 CEST 2017
Hi,
I'm facing a strange problem. I have equilibrated my protein-ligand system
in NVT run of 20ns. The temperature curve get finely converged here. But
when I try to run NPT after that, it gives me an issue as "The sum of the
two largest charge group radii (13.169886) is larger than rlist (1.400000)".
MDP used:
title = NPT Equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = no ; Initial simulation
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 cels
nstlist = 5 ; 10 fs
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; Berendsen is not suitable for
free-energy calculations, so using this
tc-grps = Protein_ACO Water_and_ions ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT, also
weak coupling
pcoupltype = isotropic ; uniform scaling of x-y-z box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure (in bar)
compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
refcoord_scaling = com
; 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 off, as continuing
from NVT
gen_temp = 310 ; temperature for velocity generation
gen_seed = -1 ; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode = Linear
comm-grps = System
I don't understand why am i getting this error after successful completion
of 1st equilibration step.
Am I making any mistakes here ?
Please suggest.
Thank you
On Tue, Apr 25, 2017 at 3:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Presumably that was discussed in the tutorial you were following. The Unix
> diff tool can help with physically inspecting what is different between
> those files. But really you should already know! A good rule of thumb is
> not run a big calculation on expensive hardware
> unless you know why you are doing it.
>
> Mark
>
> On Tue, 25 Apr 2017 12:13 abhisek Mondal <abhisek.mndl at gmail.com> wrote:
>
> > Hi,
> >
> > I'm going with it.
> >
> > I still have a question. If I reconstruct the system (stripping the
> solvent
> > and thus making smaller box size) I need to go through NVT>NPT
> > equilibrations again. This part I got it.
> > The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
> > will do ?
> > What is the difference between running npt simulation with npt.mdp and
> > npt_umbrella.mdp ?
> >
> > Please help me to catch up here.
> >
> > Thank you.
> >
> > On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 4/24/17 12:56 PM, abhisek Mondal wrote:
> > >
> > >> Hello,
> > >>
> > >> I'm using the configurations generated by pulling run to re-box >
> > >> resolvate
> > >>
> > >>> ion addition > EM > npt_umbrella(10ns) and forward.
> > >>>
> > >>
> > >> So, please clarify me something. Am I following correct path ? Should
> I
> > >> have given a npt equilibration step prior to npt_umbrella step ?
> > >>
> > >>
> > > Yes, as Mark said, you're essentially building all new simulation
> > systems.
> > > Since this is part of an umbrella sampling series, be sure you're
> getting
> > > the same (or at least, very similar) number of water molecules in each
> > box.
> > >
> > > -Justin
> > >
> > > Thank you.
> > >>
> > >> On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham <
> mark.j.abraham at gmail.com
> > >
> > >> wrote:
> > >>
> > >> Hi,
> > >>>
> > >>> I already answered that. You're effectively starting again, so do
> that.
> > >>>
> > >>> Mark
> > >>>
> > >>> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <
> > abhisek.mndl at gmail.com>
> > >>> wrote:
> > >>>
> > >>> Ok, I got it this time.
> > >>>> But what kind of equilibration I'm to perform on these stripped
> > >>>>
> > >>> structures.
> > >>>
> > >>>> Should I perform normal NPT equilibration as done before generating
> > >>>> configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c
> > >>>>
> > >>> conf0.gro
> > >>>
> > >>>> -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from
> > tutorial
> > >>>> page) and followed by mdrun step ?
> > >>>>
> > >>>>
> > >>>> ....
> > >>>
> > >>>
> > --
> > Gromacs Users mailing list
> >
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--
Abhisek Mondal
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
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