Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian) (andrian)

[Groenhof, Gerrit]

Hi,


Not sure if it was also you, but I recall replying not so long ago to a QM/MM 
question that all QM atoms must by inside the same topology (itp or top) for 
gromacs 4 and beyond. Splitting the QM atoms over multiple topologies leads to 
erroneous behaviour.

I don't know for sure if this is also the reason for the crahs, but considering 
that the some atoms are missing some forces it could be.

Best,
gerrit

Today's Topics:

   1. Re: 5. LINCS warning of QMMM simulation (andrian) (andrian)



Hi Gerrit and all users,

do you have an idea about this problem ? now, i attached all my
simulation files... hope someone can help.. thanks in advance


cheers


On 27/04/16 01:48, Groenhof, Gerrit wrote:
> Hi,
>
> Are you able to run a stable MM simulation with that system?
>
> Can you rule out that the system is not strained somewhere?
>
> Where do the starting coordinates come from?
>
> best,
>
> Gerrit
>
>
> Message: 5
> Date: Tue, 26 Apr 2016 22:39:22 +0700
> From: andrian 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] LINCS warning of QMMM simulation
> Message-ID: <571f8baa.30...@gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear gromacs users
>
> i was trying to simulate simple QMMM of 2-chlorobutanol versus
> protonated water... my simulation was going well until LINCS warning
> appeared.
>
> "Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
> after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
> that rotated more than 30 degrees"
>
> i dont know whats the problem with the system or mdp setting...
>
> any kind of help is really appreciated... thank you
>
> cheers
>
> *
> here is my mdp file
> title= my_mdp_file
> cpp  = /lib/cpp
> include  =
> define   =
>
> integrator   = md
> tinit= 0
> dt   = 0.0005
> nsteps   = 1000 ; 2ps
> nstcomm  = 10
> comm_grps= system
>
> nstxout  = 10
> nstvout  = 10
> nstfout  = 10
> nstlog   = 10
> nstenergy= 10
> nstcalcenergy = 10
> nstxtcout= 10
> xtc_grps = system
> energygrps   = QMatoms MMatoms
>
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1
>
> coulombtype  = Reaction-Field
> rcoulomb = 1
> epsilon_r= 1
> epsilon_rf = 50
> vdwtype  = cut-off
> rvdw = 1
> fourierspacing = 0.12
> pme-order = 4
> ewald-rtol = 1e-5
> couple-intramol = no
>
> tcoupl   = v-rescale
> tc-grps  = MMatoms QMatoms
> tau_t= 0.1 0  ; uncoupled QM atoms
> ref_t= 300 300
> pcoupl   = Berendsen
> pcoupltype   = isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
>
> QMMM = yes
> QMMM-grps= QMatoms
> QMmethod = RHF
> QMbasis  = STO-3G
> QMMMscheme   = normal
> QMcharge = 1
> QMmult = 1
>
> gen_vel  = no
> gen_temp = 300
> gen_seed = 173529
>
> constraints  = all-bonds
> constraint_algorithm = LINCS
> continuation = no
> shake_sor = no
> shake_tol= 0.0005
> lincs_order  = 4
> lincs_iter = 1
> lincs_warnangle  = 30
> morse= no
> *
>
> ***
> here is my topol.top
>
> ; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> 1   2   yes 0.5 0.8333
>
> ; Include alkohol_GMX.itp topology
> #include "alkohol.acpype/alkohol_GMX.itp"
>
> ; Include Position restraint file
> #ifdef POSRES_ALKOHOL
> #include "posre_alkohol.itp"
> #endif
>
> #include "waterH.acpype/waterH_GMX.itp"
>
> ; Include Position restraint file
> #ifdef POSRES_WATER
> #include "posre_water.itp"
> #endif
>
> [ system ]
>alkohol
>
> [ molecules ]
> ; Compoundnmols
> alkohol   1
> waterH  1
> 
>
> *
> here is my alkohol itp file
>
> ; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016
>
> [ atomtypes ]
> ;name   bond_type at.nummass charge   ptype   sigma
> epsilon   Amb
>c3   c3  60.0  0.0   A 3.39967e-01 

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[Justin Lemkul]

On 4/27/16 11:06 AM, andrian wrote:

Hi,

anyone can help me ??? :(



People contribute to this list when free time allows; GROMACS provides no 
promise of immediate technical support.  Perhaps the people who can best answer 
your question are busy, sleeping, or only subscribe to digests that come every 
few hours.  Be patient and don't spam the list with pleas for help.


-Justin


On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ 

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

anyone can help me ??? :(

On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
   alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
   1   c3 1   UNL C1 0.122400 12.01000 ; qtot 0.122
   2   c3 1   UNLC12 0.015700 12.01000 ; qtot 0.138
   3   h1 1   UNL H3 0.058200  

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi Gerrit and all users,

do you have an idea about this problem ? now, i attached all my 
simulation files... hope someone can help.. thanks in advance



cheers


On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
   alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
   1   c3 1   UNL C1 0.122400 12.01000 ; qtot 0.122
 

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi Gerrit and all users,

do you have an idea about this problem ? now, i attached all my 
simulation files... hope someone can help.. thanks in advance



cheers


On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
   alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
   1   c3 1   UNL C1 0.122400 12.01000 ; qtot 0.122
 

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..


*
here is my equilibrated structure (strarting configuration for qmmm)
Grunge ROck MAChoS
   20
1UNL  C1   2.600   2.380   2.439
1UNL C12   2.540   2.521   2.421
1UNL  H3   2.554   2.304   2.376
1UNL  O4   2.587   2.339   2.575
1UNL H15   2.708   2.376   2.422
1UNL C26   2.388   2.522   2.440
1UNL H27   2.554   2.559   2.319
1UNL CL8   2.612   2.651   2.519
1UNL C39   2.327   2.649   2.379
1UNL H3   10   2.363   2.497   2.543
1UNL H4   11   2.354   2.441   2.375
1UNL H5   12   2.287   2.725   2.447
1UNL H6   13   2.241   2.628   2.315
1UNL H7   14   2.400   2.708   2.323
1UNL H8   15   2.565   2.244   2.568
1UNL LA   16   2.464   2.521   2.430
2HOH  O   17   2.592   2.475   2.796
2HOH  H   18   2.684   2.494   2.769
2HOH H1   19   2.589   2.419   2.716
2HOH H2   20   2.560   2.560   2.760
   5.0   5.0   5.0
**
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..


do you have an idea ?

Cheers




On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include 

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..


*
here is my equilibrated structure (strarting configuration for qmmm)
Grunge ROck MAChoS
   20
1UNL  C1   2.600   2.380   2.439
1UNL C12   2.540   2.521   2.421
1UNL  H3   2.554   2.304   2.376
1UNL  O4   2.587   2.339   2.575
1UNL H15   2.708   2.376   2.422
1UNL C26   2.388   2.522   2.440
1UNL H27   2.554   2.559   2.319
1UNL CL8   2.612   2.651   2.519
1UNL C39   2.327   2.649   2.379
1UNL H3   10   2.363   2.497   2.543
1UNL H4   11   2.354   2.441   2.375
1UNL H5   12   2.287   2.725   2.447
1UNL H6   13   2.241   2.628   2.315
1UNL H7   14   2.400   2.708   2.323
1UNL H8   15   2.565   2.244   2.568
1UNL LA   16   2.464   2.521   2.430
2HOH  O   17   2.592   2.475   2.796
2HOH  H   18   2.684   2.494   2.769
2HOH H1   19   2.589   2.419   2.716
2HOH H2   20   2.560   2.560   2.760
   5.0   5.0   5.0
**
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..


do you have an idea ?

Cheers



On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include