[gmx-users] Issues of NEMD + 1/viscosity from g_energy
shikha nangia
nshikha at yahoo.com
Sat Apr 16 22:31:54 CEST 2011
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
----
-------
-------------------------------------------------------
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>/* 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, 3:06 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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