[gmx-users] Re: LINCS WARNING relative constraint deviation

2011-06-19 Thread E. Nihal Korkmaz 
I also checked the output of the minimization:

Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.81875038188621e+04
Maximum force =  3.20769543152855e+02 on atom 331
Norm of force =  2.04356801849931e+01

I assume the structure is not relaxed enough to start a simulation. How can
I get it minimize further? I increased the step size up to 0.1 ps, i still
get the same result.

Thanks,
Nihal

On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz
wrote:

> Dear all,
>
> I am trying to simulate a GB simulation of a 112 amino acid long protein. I
> keep getting these errors,
>
> Step 27718, time 55.436 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 33.319842, max 438.763717 (between atoms 79 and 81)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 27718, time 55.436 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.058237, max 1.390675 (between atoms 91 and 93)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  91 92   50.20.1016   0.1065  0.1010
>  91 93   90.00.1002   0.2415  0.1010
>  91 94   70.20.1025   0.1066  0.1010
>  79 80   90.00.1057   1.0667  0.1090
>  79 81   90.01.3066  47.9342  0.1090
>  85 86   90.00.1084   0.1758  0.1090
>  85 87   90.01.0654   0.1668  0.1090
>  88 89   90.00.1097   0.6994  0.1090
>  88 90   90.00.1125   0.1097  0.1090
>  91 92   50.20.1016   0.1065  0.1010
>  91 93   90.00.1002   0.2415  0.1010
>  91 94   70.20.1025   0.1066  0.1010
>
>
> I am copying my mdp parameters below, I'd appreciate any suggestions to fix
> that.
>
> integrator   = sd
> tinit= 0
> dt   = 0.002
> nsteps   = 250
> simulation_part  = 1
> init_step= 1
>
> nstxout  = 5000
> nstvout  = 5000
> nstenergy= 500
> nstxtcout= 500
> nstlog   = 500
>
> xtc_grps = System
> energygrps   = System
> comm_mode= Linear
> ; neighbor searching and vdw/pme setting up
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 2.0
>
> implicit_solvent = GBSA
> gb_algorithm = OBC
> gb_saltconc  = 0.15
> rgbradii = 2.0
>
> coulombtype  = Cut-off
> fourierspacing   = 0.1
> pme_order= 6
> rcoulomb = 2.0
>
> vdwtype  = Cut-off
> rvdw_switch  = 1.0
> rvdw = 2.0
>
> ; cpt control
> tcoupl   = V-rescale
> tc-grps  = System
> tau_t= 0.1
> ref_t= 300.0
>
> Pcoupl   = Berendsen
> pcoupltype   = isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
>
> ; velocity & temperature control
> gen_vel  = yes
> gen_temp = 300.0
> annealing= no
> constraints  = hbonds
> constraint_algorithm = lincs
> morse= no
>
>
> Thanks,
> --
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email:   kork...@wisc.edu
>
>
>


-- 
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   kork...@wisc.edu
-- 
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Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

2011-06-20 Thread Mark Abraham 

On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:

I also checked the output of the minimization:

Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.81875038188621e+04
Maximum force =  3.20769543152855e+02 on atom 331
Norm of force =  2.04356801849931e+01

I assume the structure is not relaxed enough to start a simulation. 
How can I get it minimize further? I increased the step size up to 0.1 
ps, i still get the same result.


The minimization is probably OK, but a period of equilibration at a 
short time step will probably help smooth the process out. Simulations 
in implicit solvent have few explicit degrees of freedom compared to 
explicit solvent, and might be rather more susceptible to equilibration 
issues if the generated velocities are randomly not-quite-good-enough.


Mark


Thanks,
Nihal

On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz 
mailto:enihalkork...@gmail.com>> wrote:


Dear all,

I am trying to simulate a GB simulation of a 112 amino acid long
protein. I keep getting these errors,

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010
 79 80   90.00.1057   1.0667  0.1090
 79 81   90.01.3066  47.9342  0.1090
 85 86   90.00.1084   0.1758  0.1090
 85 87   90.01.0654   0.1668  0.1090
 88 89   90.00.1097   0.6994  0.1090
 88 90   90.00.1125   0.1097  0.1090
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010


I am copying my mdp parameters below, I'd appreciate any
suggestions to fix that.

integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 250
simulation_part  = 1
init_step= 1

nstxout  = 5000
nstvout  = 5000
nstenergy= 500
nstxtcout= 500
nstlog   = 500

xtc_grps = System
energygrps   = System
comm_mode= Linear
; neighbor searching and vdw/pme setting up
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 2.0

implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc  = 0.15
rgbradii = 2.0

coulombtype  = Cut-off
fourierspacing   = 0.1
pme_order= 6
rcoulomb = 2.0

vdwtype  = Cut-off
rvdw_switch  = 1.0
rvdw = 2.0

; cpt control
tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; velocity & temperature control
gen_vel  = yes
gen_temp = 300.0
annealing= no
constraints  = hbonds
constraint_algorithm = lincs
morse= no


Thanks,
-- 
Elif Nihal Korkmaz


Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 
Email: kork...@wisc.edu 





--
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 
Email: kork...@wisc.edu 




-- 
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Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

2011-06-20 Thread E. Nihal Korkmaz 
What would you suggest as a short time step? I was using 0.002 ps. And just
to make sure, would 5 ns of equilibration be enough for a ~110 amino acid
long protein?

Thanks,
Nihal

On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham wrote:

> **
> On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
>
> I also checked the output of the minimization:
>
> Steepest Descents converged to machine precision in 402 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -1.81875038188621e+04
> Maximum force =  3.20769543152855e+02 on atom 331
> Norm of force =  2.04356801849931e+01
>
> I assume the structure is not relaxed enough to start a simulation. How can
> I get it minimize further? I increased the step size up to 0.1 ps, i still
> get the same result.
>
>
> The minimization is probably OK, but a period of equilibration at a short
> time step will probably help smooth the process out. Simulations in implicit
> solvent have few explicit degrees of freedom compared to explicit solvent,
> and might be rather more susceptible to equilibration issues if the
> generated velocities are randomly not-quite-good-enough.
>
> Mark
>
>
> Thanks,
> Nihal
>
> On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz <
> enihalkork...@gmail.com> wrote:
>
>> Dear all,
>>
>> I am trying to simulate a GB simulation of a 112 amino acid long protein.
>> I keep getting these errors,
>>
>> Step 27718, time 55.436 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 33.319842, max 438.763717 (between atoms 79 and 81)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 27718, time 55.436 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.058237, max 1.390675 (between atoms 91 and 93)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>  91 92   50.20.1016   0.1065  0.1010
>>  91 93   90.00.1002   0.2415  0.1010
>>  91 94   70.20.1025   0.1066  0.1010
>>  79 80   90.00.1057   1.0667  0.1090
>>  79 81   90.01.3066  47.9342  0.1090
>>  85 86   90.00.1084   0.1758  0.1090
>>  85 87   90.01.0654   0.1668  0.1090
>>  88 89   90.00.1097   0.6994  0.1090
>>  88 90   90.00.1125   0.1097  0.1090
>>  91 92   50.20.1016   0.1065  0.1010
>>  91 93   90.00.1002   0.2415  0.1010
>>  91 94   70.20.1025   0.1066  0.1010
>>
>>
>> I am copying my mdp parameters below, I'd appreciate any suggestions to
>> fix that.
>>
>> integrator   = sd
>> tinit= 0
>> dt   = 0.002
>> nsteps   = 250
>> simulation_part  = 1
>> init_step= 1
>>
>> nstxout  = 5000
>> nstvout  = 5000
>> nstenergy= 500
>> nstxtcout= 500
>> nstlog   = 500
>>
>> xtc_grps = System
>> energygrps   = System
>> comm_mode= Linear
>> ; neighbor searching and vdw/pme setting up
>> nstlist  = 10
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 2.0
>>
>> implicit_solvent = GBSA
>> gb_algorithm = OBC
>> gb_saltconc  = 0.15
>> rgbradii = 2.0
>>
>> coulombtype  = Cut-off
>> fourierspacing   = 0.1
>> pme_order= 6
>> rcoulomb = 2.0
>>
>> vdwtype  = Cut-off
>> rvdw_switch  = 1.0
>> rvdw = 2.0
>>
>> ; cpt control
>> tcoupl   = V-rescale
>> tc-grps  = System
>> tau_t= 0.1
>> ref_t= 300.0
>>
>> Pcoupl   = Berendsen
>> pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>>
>> ; velocity & temperature control
>> gen_vel  = yes
>> gen_temp = 300.0
>> annealing= no
>> constraints  = hbonds
>> constraint_algorithm = lincs
>> morse= no
>>
>>
>> Thanks,
>> --
>> Elif Nihal Korkmaz
>>
>> Research Assistant
>> University of Wisconsin - Biophysics
>> Member of Qiang Cui & Thomas Record Labs
>> 1101 University Ave, Rm. 8359
>> Madison, WI 53706
>> Phone:  608-265-3644
>> Email:   kork...@wisc.edu
>>
>>
>>
>
>
> --
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email:   kork...@wisc.edu
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archiv

Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

2011-06-20 Thread Mark Abraham 

On 21/06/2011 2:10 AM, E. Nihal Korkmaz wrote:

What would you suggest as a short time step? I was using 0.002 ps.


I'd suggest starting with maybe 100ps of 0.0005 ps time steps, but 
that's probably overkill.


And just to make sure, would 5 ns of equilibration be enough for a 
~110 amino acid long protein?


I guess so. It's cheap.

Mark


Thanks,
Nihal

On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham > wrote:


On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:

I also checked the output of the minimization:

Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.81875038188621e+04
Maximum force =  3.20769543152855e+02 on atom 331
Norm of force =  2.04356801849931e+01

I assume the structure is not relaxed enough to start a
simulation. How can I get it minimize further? I increased the
step size up to 0.1 ps, i still get the same result.


The minimization is probably OK, but a period of equilibration at
a short time step will probably help smooth the process out.
Simulations in implicit solvent have few explicit degrees of
freedom compared to explicit solvent, and might be rather more
susceptible to equilibration issues if the generated velocities
are randomly not-quite-good-enough.

Mark



Thanks,
Nihal

On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz
mailto:enihalkork...@gmail.com>> wrote:

Dear all,

I am trying to simulate a GB simulation of a 112 amino acid
long protein. I keep getting these errors,

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010
 79 80   90.00.1057   1.0667  0.1090
 79 81   90.01.3066  47.9342  0.1090
 85 86   90.00.1084   0.1758  0.1090
 85 87   90.01.0654   0.1668  0.1090
 88 89   90.00.1097   0.6994  0.1090
 88 90   90.00.1125   0.1097  0.1090
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010


I am copying my mdp parameters below, I'd appreciate any
suggestions to fix that.

integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 250
simulation_part  = 1
init_step= 1

nstxout  = 5000
nstvout  = 5000
nstenergy= 500
nstxtcout= 500
nstlog   = 500

xtc_grps = System
energygrps   = System
comm_mode= Linear
; neighbor searching and vdw/pme setting up
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 2.0

implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc  = 0.15
rgbradii = 2.0

coulombtype  = Cut-off
fourierspacing   = 0.1
pme_order= 6
rcoulomb = 2.0

vdwtype  = Cut-off
rvdw_switch  = 1.0
rvdw = 2.0

; cpt control
tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; velocity & temperature control
gen_vel  = yes
gen_temp = 300.0
annealing= no
constraints  = hbonds
constraint_algorithm = lincs
morse= no


Thanks,
-- 
Elif Nihal Korkmaz