[gmx-users] LINCS error

[Mark Abraham]

On 19/12/2011 1:05 AM, aiswarya pawar wrote:
> Hi users,
>
> I did energy minimization of a protein complex using the following 
> minimization mdp file.

See 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation 
for general advice.

>
> ; 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

You are asking for trouble by generating velocities and doing position 
restraints with P-R pressure coupling in one step. It might work, but 
the workflow in the above link is safer.

>
> 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

Why are you re-generating non-equilibrium velocities after equilibrating 
them?

Mark

>
>
> 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
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111219/f4b07dd9/attachment.html>