[gmx-users] Issues of NEMD + 1/viscosity from g_energy
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 16 22:34:26 CEST 2011
shikha nangia wrote:
> Thanks again, Justin.
>
> Dear all,
>
> I figured out the problem. Error was in my mdp file options. I did not
> specify the acc-groups correctly. I can get 1/viscosity using g_energy.
>
> However, once the acc-groups are specified, now the NEW issue is not
> being able to run my job correctly.
>
> I get the following errors:
>
> Step 376, time 7.52 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.006964, max 0.163855 (between atoms 861 and 859)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
>
Whatever you're doing to the system is causing its underlying model physics to
break down. Please see:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
If you want help troubleshooting, please provide:
1. A description of the system
2. Outcomes of energy minimization and equilibration
3. Full .mdp file of the process that is crashing
-Justin
> ----
> -------
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: domdec.c, line: 4124
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
>
> ---------------
>
> I did not have any problems in my equilibrium simulations...this is
> happening in NEMD simulations.
>
> Here is my .mdp file
>
> title = Martini
> cpp = /usr/bin/cpp
> integrator = md
> tinit = 0.0
> dt = 0.01
> nsteps = 500
> nstcomm = 1
> comm-grps = system
> nstxout = 10
> nstvout = 10
> nstfout = 10
> nstlog = 10
> nstenergy = 10
> nstxtcout = 2500
> xtc_precision = 100
> xtc-grps =
> energygrps = system
> nstlist = 1
> ns_type = grid
> pbc = xyz
> rlist = 1.7
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r = 15
> vdw_type = Shift
> rvdw_switch = 0.9
> rvdw = 1.2
> DispCorr = EnerPres
> tcoupl = V-rescale
> tc-grps = NGL W
> tau_t = 1.0 1.0
> ref_t = 300. 300.
> Pcoupl = No
> Pcoupltype = Isotropic
> tau_p = 1.0
> compressibility = 1e-5
> ref_p = 1.0
> gen_vel = Yes
> gen_temp = 300
> gen_seed = 473529
> constraints = None
> constraint_algorithm = Lincs
> unconstrained_start = no
> lincs_order = 1
> lincs_warnangle = 30
>
> ; Non-equilibrium MD stuff
> acc-grps = NGL W
> accelerate = 0.1 0 0 -0.1 0 0
> freezegrps =
> freezedim =
> cos_acceleration = 0.1
> deform =
>
> Best,
> SN
>
> --- On *Sat, 4/16/11, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] 1/viscosity from g_energy
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Saturday, April 16, 2011, 3:27 PM
>
>
>
> shikha nangia wrote:
> > Thanks for your instant reply, Justin.
> >
> > Dear all,
> >
> > Please correct me if I am woring here....but...reading through
> the user-list, I gathered that -vis option og g_energy oes not give
> good results and instead cos_accleration should be used from the
> following reference.
> >
> >> /@Article{Hess2002b,
> > />/ author = {B. Hess},
> > />/ title = {Determining the shear viscosity of model
> liquids from />/molecular simulation},
> > />/ journal = {J. Chem. Phys.},
> > />/ year = 2002,
> > />/ volume = 116,
> > />/ pages = {209-217}
> > />/}
> > /
> >
> > I am trying to get the results of viscosity through
> cos_acceleration that probably are formatted as below (taken from a
> user-list).
> >
> >> / Energy Average Err.Est. RMSD
> > Tot-Drift
> > />/
> -------------------------------------------------------------------------------
> > />/ 1/Viscosity / (/ s/kg)
> > /
> >
> >
>
> If the proper output options are not there, then there may have been
> a problem in the .mdp file that prevented the correct energy terms
> from being written. If present in the .edr file, it should be shown
> in the list (sorry, I was thinking of something else). Please post
> your .mdp file.
>
> -Justin
>
> > Thanks again,
> >
> > SN
> >
> > --- On *Sat, 4/16/11, Justin A. Lemkul /<jalemkul at vt.edu
> </mc/compose?to=jalemkul at vt.edu>>/* wrote:
> >
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu
> </mc/compose?to=jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] 1/viscosity from g_energy
> > To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>>
> > Date: Saturday, April 16, 2011, 3:06 PM
> >
> >
> >
> > shikha nangia wrote:
> > > Dear gmx-users,
> > >
> > > I am trying to obtain 1/viscosity values for my system after
> > using the cos_acceleration option in the mdp file. My gromacs
> > version is 4.5.4 released on March 21, 2011.
> > > When I try using the g_energy option for my file
> > >
> > > g_energy -f ener.edr -o outfile.xvg
> > >
> > > I get the following options
> > >
> > > End your selection with an empty line or a zero.
> > >
> -------------------------------------------------------------------
> > > 1 Bond 2 Angle 3
> Improper-Dih. 4 LJ-(SR) 5 Disper.-corr. 6
> Coulomb-(SR) 7 Potential 8 Kinetic-En. 9
> Total-Energy 10 Conserved-En. 11 Temperature 12
> Pres.-DC 13 Pressure 14 Box-XX 15 Box-YY
> 16 Box-ZZ 17 Box-YX 18 Box-ZX
> 19 Box-ZY 20 Volume 21 Density 22 pV
> 23 Enthalpy 24 Vir-XX 25 Vir-XY
> 26 Vir-XZ 27 Vir-YX 28 Vir-YY 29
> Vir-YZ 30 Vir-ZX 31 Vir-ZY 32
> Vir-ZZ 33 Pres-XX 34 Pres-XY 35
> Pres-XZ 36 Pres-YX 37 Pres-YY 38
> Pres-YZ 39 Pres-ZX 40 Pres-ZY 41
> Pres-ZZ 42 #Surf*SurfTen 43 Mu-X 44 Mu-Y
> 45 Mu-Z 46 T-System 47 Lamb-System
> >
> > > I am not sure which option (1 to 47) gives 1/viscosity. I
> tried
> > looking through the manual and searching the user list but
> could not
> > resolve the issue.
> > >
> > > Please let me know what am I missing here.
> > >
> >
> > Use -vis rather than -o.
> >
> > -Justin
> >
> > > Thanks,
> > > SN
> > >
> > >
> >
> > -- ========================================
> >
> > 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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>
> -- ========================================
>
> 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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--
========================================
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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