[gmx-users] Re: LINCS error

[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 <aiswarya.pawar at gmail.com>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 = 2500000 ; 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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