Re: [gmx-users] LINCS WARNING during EPM2 CO2 Simulation

2017-10-19 Thread Mark Abraham 
Hi,

Simplify things until you identify the problematic part. Eg do one CO2
molecule first.

Mark

On Thu, 19 Oct 2017 03:16 Pimo Oni  wrote:

> Dear community members,
>
> Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
> I met continual LINCS WARNING. I've been struggling for more than week but
> make no progress in fixing it.. : (
>
> Here attach my pdb, top, and mdp files below.
> I would much appreciate any tip & comments.
>
> Thanks
> Pimo
>
> -
>
> ***command used***
>
> gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5
> 5 5 -nmol 999
>
> gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o
> testco2em.tpr
>
> gmx_d mdrun -s testco2em.tpr -deffnm testco2em
>
> ***error***
> Step 12, time 0.012 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.00, max 0.00 (between atoms 2201 and 2202)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 22   48.50.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>
> ***co2EPM2.pdb***
> TITLE CO2 with dummy masses
> REMARKTHIS IS A SIMULATION BOX
> CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1
> MODEL1
> ATOM  1  M1  CO2 1   0.171   0.000   0.000  1.00  0.00
>
> ATOM  2  M2  CO2 1   2.149   0.000   0.000  1.00  0.00
>
> ATOM  3  C   CO2 1   1.160   0.000   0.000  1.00  0.00
>
> ATOM  4  O1  CO2 1   0.000   0.000   0.000  1.00  0.00
>
> ATOM  5  O2  CO2 1   2.320   0.000   0.000  1.00  0.00
>
> TER
> ENDMDL
>
> ***co2EPM2.top***
> [ defaults ]
> ; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
>   1   2  no 1.0  1.0
>
>  [ atomtypes ]
> ; type  mass charge  ptype sigma(nm) epsilon(kJ/M)
>   M 22.00475  0. A 0.0   0.
>   C  0.0  0.6512 V 0.27570   0.2339
>   O  0.0 -0.3256 V 0.30330   0.6694
>
>
> [ moleculetype ]
> ; name nrexcl
>   CO2  2
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge  mass
>   1  M1 CO2M1   1 0. 22.00475
>   2  M1 CO2M2   1 0. 22.00475
>   3  C1 CO2C1 0.6512  0.0
>   4  O1 CO2O1   1-0.3256  0.0
>   5  O1 CO2O2   1-0.3256  0.0
>
> [ constraints ]
> ; ai aj funct distance
>   1  2  1 0.1978252
>
> [ virtual_sites2 ]
> ; ai aj ak funct a
>   3  1  2  1 0.5000
>   4  1  2  1 1.086376
>   5  2  1  1 1.086376
>
> [ exclusions ]
> 3 4 5
> 4 5 3
> 5 4 3
>
> [ system ]
> CO2EPM2
>
> [ molecules ]
> ; name nmol
>   CO2  1000
>
> ***em.mdp***
> define   =
>
> ; RUN CONTROL PARAMETERS
> integrator   = steep
> tinit= 0
> dt   = 0.001
> nsteps   = -1
> init_step= 0
> simulation_part  = 1
> comm-mode= Linear
> nstcomm  = 100
> comm-grps=
>
> emtol= 10.0
> emstep   = 0.01
> niter= 20
> fcstep   = 0
> nstcgsteep   = 1000
> nbfgscorr= 10
> energygrps   = system
>
> cutoff-scheme= Verlet
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> periodic_molecules   = no
> verlet-buffer-tolerance  = -1
> rlist= 1.5
> rlistlong= -1
> nstcalclr= -1
>
> ; Method for doing electrostatics
> coulombtype  = PME
> coulomb-modifier = Potential-shift-Verlet
> rcoulomb-switch  = 0
> rcoulomb = 1.5
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1
> epsilon_rf   = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> vdw-modifier = Potential-shift-Verlet
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 1.5
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = no
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Separate tables between energy group pairs
> energygrp-table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald-rtol-lj= 0.001
> lj-pme-comb-rule

[gmx-users] LINCS WARNING during EPM2 CO2 Simulation

2017-10-18 Thread Pimo Oni 
Dear community members,

Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
I met continual LINCS WARNING. I've been struggling for more than week but
make no progress in fixing it.. : (

Here attach my pdb, top, and mdp files below.
I would much appreciate any tip & comments.

Thanks
Pimo

-

***command used***

gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5
5 5 -nmol 999

gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o
testco2em.tpr

gmx_d mdrun -s testco2em.tpr -deffnm testco2em

***error***
Step 12, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.00 (between atoms 2201 and 2202)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 22   48.50.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978

***co2EPM2.pdb***
TITLE CO2 with dummy masses
REMARKTHIS IS A SIMULATION BOX
CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  M1  CO2 1   0.171   0.000   0.000  1.00  0.00

ATOM  2  M2  CO2 1   2.149   0.000   0.000  1.00  0.00

ATOM  3  C   CO2 1   1.160   0.000   0.000  1.00  0.00

ATOM  4  O1  CO2 1   0.000   0.000   0.000  1.00  0.00

ATOM  5  O2  CO2 1   2.320   0.000   0.000  1.00  0.00

TER
ENDMDL

***co2EPM2.top***
[ defaults ]
; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
  1   2  no 1.0  1.0

 [ atomtypes ]
; type  mass charge  ptype sigma(nm) epsilon(kJ/M)
  M 22.00475  0. A 0.0   0.
  C  0.0  0.6512 V 0.27570   0.2339
  O  0.0 -0.3256 V 0.30330   0.6694


[ moleculetype ]
; name nrexcl
  CO2  2

[ atoms ]
; nr type resnr residu atom cgnr charge  mass
  1  M1 CO2M1   1 0. 22.00475
  2  M1 CO2M2   1 0. 22.00475
  3  C1 CO2C1 0.6512  0.0
  4  O1 CO2O1   1-0.3256  0.0
  5  O1 CO2O2   1-0.3256  0.0

[ constraints ]
; ai aj funct distance
  1  2  1 0.1978252

[ virtual_sites2 ]
; ai aj ak funct a
  3  1  2  1 0.5000
  4  1  2  1 1.086376
  5  2  1  1 1.086376

[ exclusions ]
3 4 5
4 5 3
5 4 3

[ system ]
CO2EPM2

[ molecules ]
; name nmol
  CO2  1000

***em.mdp***
define   =

; RUN CONTROL PARAMETERS
integrator   = steep
tinit= 0
dt   = 0.001
nsteps   = -1
init_step= 0
simulation_part  = 1
comm-mode= Linear
nstcomm  = 100
comm-grps=

emtol= 10.0
emstep   = 0.01
niter= 20
fcstep   = 0
nstcgsteep   = 1000
nbfgscorr= 10
energygrps   = system

cutoff-scheme= Verlet
nstlist  = 10
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
verlet-buffer-tolerance  = -1
rlist= 1.5
rlistlong= -1
nstcalclr= -1

; Method for doing electrostatics
coulombtype  = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch  = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald_geometry   = 3d
epsilon_surface  = 0

; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau-t= 1
ref-t= 300
; pressure coupling
Pcoupl   = no