Re: [gmx-users] Re: LINCS error

2011-12-21 Thread aiswarya . pawar
I did few changes ie decreased the time step/ increased the equilibration 
steps/ omitted the generation of velocity in production run / did 2 steps of 
equilibration / checked the starting structure for steric clashes. 

I don't understand what else should I try to fix the lincs warnings.


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-Original Message-
From: Mark Abraham 
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 21 Dec 2011 00:15:15 
To: Discussion list for GROMACS users
Reply-To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Re: LINCS error

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Re: [gmx-users] Re: LINCS error

2011-12-20 Thread Mark Abraham


On 20/12/11, aiswarya pawar   wrote:
> i went through the mailing list, but i dont understand when i run the same 
> protein on my computer it runs correctly without any LINCS warning. On the 
> cluster with 64 processors the job runs but crashes in between and shows the 
> LINCS warning. 
> 


That happens. Your different computers are running different versions of the 
calculation. Numerical artefacts do happen, especially if you use algorithms 
that are known to be unstable when not in equilibrium, like I said three days 
ago. Why have you repeated your question instead of trying my suggestion?



> Please anyone tell me what could be the reason. Is anything wrong with my 
> protein.
> 


Something is very likely wrong with your system preparation. The links people 
have been giving you detail the advice on how to diagnose the problem or how to 
be more gentle. There's little else for me to say.


Mark 

> 
> 
> 
> On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar  
> wrote:
> 
> 
> > Hi users,
> > 
> > I did energy minimization of a protein complex using the following 
> > minimization mdp file.
> > 
> > 
> > 
> > ; Lines starting with ';' ARE COMMENTS
> > ; Everything following ';' is also comment
> > 
> > 
> > 
> > title   = Energy Minimization   ; Title of run
> > 
> > 
> > ; The following line tell the program the standard locations where to find 
> > certain files
> > 
> > 
> > cpp = /lib/cpp  ; Preprocessor
> > 
> > 
> > 
> > 
> > ; Define can be used to control processes
> > 
> > define          = -DFLEXIBLE
> > 
> > 
> > ; Parameters describing what to do, when to stop and what to save
> > integrator  = steep ; Algorithm (steep = steepest descent 
> > minimization)
> > 
> > 
> > emtol   = 1000.0    ; Stop minimization when the maximum 
> > force < 1.0 kJ/mol
> > emstep      = 0.01
> > 
> > nsteps  = 5000  ; Maximum number of (minimization) 
> > steps to perform
> > nstenergy   = 10; Write energies to disk every nstenergy steps
> > 
> > 
> > energygrps  = Protein   ; Which energy group(s) to write to disk
> > 
> > 
> > ; Parameters describing how to find the neighbors of each atom and how to 
> > calculate the interactions
> > 
> > 
> > nstlist = 10; Frequency to update the neighbor list 
> > and long range forces
> > ns_type = grid  ; Method to determine neighbor list 
> > (simple, grid)
> > 
> > 
> > rlist   = 1.0   ; Cut-off for making neighbor list 
> > (short range forces)
> > coulombtype = PME   ; Treatment of long range electrostatic 
> > interactions
> > 
> > 
> > rcoulomb= 1.0   ; long range electrostatic cut-off
> > rvdw= 1.4   ; long range Van der Waals cut-off
> > 
> > 
> > constraints = none  ; Bond types to replace by constraints
> > pbc     = xyz   ; Periodic Boundary Conditions (yes/no)
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > and the pr.mdp =
> > 
> > 
> > ; VARIOUS PREPROCESSING OPTIONS
> > title                    = Position Restrained Molecular Dynamics
> > define                   = -DPOSRES
> > 
> > 
> > 
> > 
> > constraints              = all-bonds
> > integrator               = md
> > dt                       = 0.001 ; ps !
> > nsteps                   = 25000 ; total 50 ps.
> > nstcomm                  = 10
> > 
> > 
> > nstxout                  = 500 ; collect data every 1 ps
> > nstxtcout                = 500
> > nstvout                  = 0
> > nstfout                  = 0
> > nstlist                  = 10
> > 
> > 
> > ns_type                  = grid
> > rlist                    = 1.0
> > coulombtype              = PME
> > rcoulomb                 = 1.0
> > vdwtype                  = cut-off
> > rvdw                     = 1.4
> > 
> > 
> > pme_order                = 4
> > ewald_rtol               = 1e-5
> > optimize_fft             = yes
> > DispCorr                 = no
> > ; Berendsen temperature coupling is on
> > Tcoupl                   = v-rescale
> > 
> > 
> > tau_t                    = 0.1 0.1
> > tc-grps = protein non-protein
> > ref_t                    = 300 300
> > ; Pressure coupling is on
> > Pcoupl                   = parrinello-rahman
> > 
> > 
> > Pcoupltype               = isotropic
> > tau_p                    = 1.0
> > compressibility          = 4.5e-5
> > ref_p                    = 1.0
> > ; Generate velocites is on at 300 K.
> > 
> > 
> > gen_vel                  = yes
> > gen_temp                 = 300.0
> > gen_seed                 = -1
> > 
> > 
> > 
> > 
> > and md.mdp file =
> > 
> > 
> > ; VARIOUS PREPROCESSING OPTIONS
> > 
> > 
> > title                    = Position Restrained Molecular Dynamics
> > 
> > 
> > 
> > 
> > ; RUN CONTROL PARAMETERS
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; 2fs !
> > 
> > 
> > nsteps = 250 ; total 5000 ps.
> > nstcomm = 10
> > nstxout = 500 ; collect data every 1 ps
> 

[gmx-users] Re: LINCS error

2011-12-20 Thread aiswarya pawar
i went through the mailing list, but i dont understand when i run the same
protein on my computer it runs correctly without any LINCS warning. On the
cluster with 64 processors the job runs but crashes in between and shows
the LINCS warning.


Please anyone tell me what could be the reason. Is anything wrong with my
protein.


On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar wrote:

> Hi users,
>
> I did energy minimization of a protein complex using the following
> minimization mdp file.
>
> ; Lines starting with ';' ARE COMMENTS
> ; Everything following ';' is also comment
>
> title = Energy Minimization ; Title of run
>
> ; The following line tell the program the standard locations where to find
> certain files
> cpp = /lib/cpp ; Preprocessor
>
>
> ; Define can be used to control processes
> define  = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0   ; Stop minimization when the maximum force < 1.0 kJ/mol
> emstep  = 0.01
> nsteps = 5000 ; Maximum number of (minimization) steps to perform
> nstenergy = 10 ; Write energies to disk every nstenergy steps
> energygrps = Protein ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 10 ; Frequency to update the neighbor list and long range forces
> ns_type = grid   ; Method to determine neighbor list (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME   ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0 ; long range electrostatic cut-off
> rvdw = 1.4 ; long range Van der Waals cut-off
> constraints = none ; Bond types to replace by constraints
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
>
> and the pr.mdp =
>
> ; VARIOUS PREPROCESSING OPTIONS
> title= Position Restrained Molecular Dynamics
> define   = -DPOSRES
>
> constraints  = all-bonds
> integrator   = md
> dt   = 0.001 ; ps !
> nsteps   = 25000 ; total 50 ps.
> nstcomm  = 10
> nstxout  = 500 ; collect data every 1 ps
> nstxtcout= 500
> nstvout  = 0
> nstfout  = 0
> nstlist  = 10
> ns_type  = grid
> rlist= 1.0
> coulombtype  = PME
> rcoulomb = 1.0
> vdwtype  = cut-off
> rvdw = 1.4
> pme_order= 4
> ewald_rtol   = 1e-5
> optimize_fft = yes
> DispCorr = no
> ; Berendsen temperature coupling is on
> Tcoupl   = v-rescale
> tau_t= 0.1 0.1
> tc-grps = protein non-protein
> ref_t= 300 300
> ; Pressure coupling is on
> Pcoupl   = parrinello-rahman
> Pcoupltype   = isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
> ; Generate velocites is on at 300 K.
> gen_vel  = yes
> gen_temp = 300.0
> gen_seed = -1
>
> and md.mdp file =
>
> ; VARIOUS PREPROCESSING OPTIONS
> title= Position Restrained Molecular Dynamics
>
>
> ; RUN CONTROL PARAMETERS
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; 2fs !
> nsteps = 250 ; total 5000 ps.
> nstcomm = 10
> nstxout = 500 ; collect data every 1 ps
> nstxtcout = 0
> nstvout = 0
> nstfout = 0
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> DispCorr = no
> ; Berendsen temperature coupling is on
> Tcoupl = v-rescale
> tau_t = 0.1 0.1
> tc-grps = protein non-protein
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = parrinello-rahman
> Pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = -1
>
>
> The minimization step went well. but while doing the final mdrun am
> getting LINCS error. i read through the numerous mailing list on grimaces
> but still couldn't understand how would i fix this. am getting this error
> for all the 10 protein complex i did minimization for. Please help.
>
>
> Thanks,
> Aiswarya
>
>
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Please search the archive at 
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