Re: [gmx-users] SHAKE error

2016-07-22 Thread gozde ergin 
No I am using same Gromacs 4.6.5. 
I run these two simulations again one runs and the other fails with the same 
.mdp file.

> On 22 Jul 2016, at 13:53, Justin Lemkul  wrote:
> 
> 
> 
> On 7/22/16 7:50 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I use md-vv and SHAKE algorithm however I face an error which I was not 
>> before.
>> Before I had 1-decanol and water system and now I have cis-pionic and water 
>> system.
>> 
>> I exactly use the same .mdp file just as before however this error comes :
>> SHAKE is not supported with domain decomposition and constraint that cross 
>> charge group boundaries, use LINCS
>> 
>> Do you have any idea why I am getting this error which I was not getting 
>> before?
>> 
> 
> Probably you were using a different version of the code before.  Various 
> feature combinations get disabled as suitable tests are not run or bugs are 
> found. LINCS is more stable, anyway, so just use it instead and the run 
> should work.
> 
> -Justin
> 
>> MDP FILE:
>> 
>> 
>> integrator   = md-vv
>> dt   = 0.002
>> nsteps   = 800   ; 16 ns
>> ; Output control
>> nstxout  = 2000
>> nstvout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> ; Bond parameters
>> continuation = no; Initial simulation
>> constraint_algorithm = shake ; holonomic constraints
>> constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
>> constrained
>> shake_tol= 0.0001
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range 
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>> ; Temperature coupling
>> ; tcoupl is implicitly handled by the sd integrator
>> tcoupl   = nose-hoover
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; Velocity generation is on
>> gen_temp= 300   ; temperature for velocity generation
>> gen_seed= -1; random seed
>> ; COM motion removal
>> ; These options remove COM motion of the system
>> nstcomm = 10
>> comm-mode   = Linear
>> comm-grps   = System
>> 
>> 
>> 
>> thanks
>> 
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
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Re: [gmx-users] SHAKE error

2016-07-22 Thread Justin Lemkul 



On 7/22/16 7:50 AM, gozde ergin wrote:

Dear all,

I use md-vv and SHAKE algorithm however I face an error which I was not before.
Before I had 1-decanol and water system and now I have cis-pionic and water 
system.

I exactly use the same .mdp file just as before however this error comes :
SHAKE is not supported with domain decomposition and constraint that cross 
charge group boundaries, use LINCS

Do you have any idea why I am getting this error which I was not getting before?



Probably you were using a different version of the code before.  Various feature 
combinations get disabled as suitable tests are not run or bugs are found. 
LINCS is more stable, anyway, so just use it instead and the run should work.


-Justin


MDP FILE:


integrator   = md-vv
dt   = 0.002
nsteps   = 800   ; 16 ns
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no; Initial simulation
constraint_algorithm = shake ; holonomic constraints
constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl   = nose-hoover
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System



thanks



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] SHAKE error

2016-07-22 Thread gozde ergin 
Dear all,

I use md-vv and SHAKE algorithm however I face an error which I was not before. 
Before I had 1-decanol and water system and now I have cis-pionic and water 
system.

I exactly use the same .mdp file just as before however this error comes : 
SHAKE is not supported with domain decomposition and constraint that cross 
charge group boundaries, use LINCS

Do you have any idea why I am getting this error which I was not getting before?

MDP FILE: 


integrator   = md-vv 
dt   = 0.002
nsteps   = 800   ; 16 ns
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no; Initial simulation 
constraint_algorithm = shake ; holonomic constraints 
constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl   = nose-hoover
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System 



thanks
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