[gmx-users] LINCS dependence
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 29 22:58:37 CEST 2009
sunny mishra wrote:
> Hi Justin,
>
> Thanks for the reply. I am doing the energy minimization of Na K pump
> with PDB ID 3B8E using MARTINI forcefield. Here is my em.mdp file for
> the same. First I get the .gro file from my cleaned PDB file and then
> try to minimize the system using grompp and then when I do mdrun it
> gives me lincs warning and gives me segmentation fault.
>
Well, if your system is crashing during EM, there is something geometrically
unresolvable about the structure. Does your structure after the MARTINI
conversion process look reasonable?
You can try setting "nstxout = 1" to try to capture frames before the crash to
see where things are falling apart.
-Justin
> ;
> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
> ;
> ; for use with GROMACS 3.3
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS =
> title = Martini
> cpp = /usr/bin/cpp
>
> ; RUN CONTROL PARAMETERS =
> ; MARTINI - Most simulations are stable with dt=40 fs,
> ; some (especially rings) require 20-30 fs.
> ; The range of time steps used for parametrization
> ; is 20-40 fs, using smaller time steps is therefore not recommended.
>
> integrator = steep
> ; start time and timestep in ps
> tinit = 0.0
> dt = 0.030
> nsteps = 1000
> ; number of steps for center of mass motion removal =
> nstcomm = 1
> comm-grps =
>
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout = 5000
> nstvout = 5000
> nstfout = 0
> ; Output frequency for energies to log file and energy file =
> nstlog = 1000
> nstenergy = 1000
> ; Output frequency and precision for xtc file =
> nstxtcout = 1000
> xtc_precision = 100
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps =
> ; Selection of energy groups =
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS =
> ; MARTINI - no need for more frequent updates
> ; or larger neighborlist cut-off due
> ; to the use of shifted potential energy functions.
>
> ; nblist update frequency =
> nstlist = 10
> ; ns algorithm (simple or grid) =
> ns_type = grid
> ; Periodic boundary conditions: xyz or none =
> pbc = xyz
> ; nblist cut-off =
> rlist = 1.2
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; MARTINI - vdw and electrostatic interactions are used
> ; in their shifted forms. Changing to other types of
> ; electrostatics will affect the general performance of
> ; the model.
>
> ; Method for doing electrostatics =
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r = 15
> ; Method for doing Van der Waals =
> vdw_type = Shift
> ; cut-off lengths =
> rvdw_switch = 0.9
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; MARTINI - normal temperature and pressure coupling schemes
> ; can be used. It is recommended to couple individual groups
> ; in your system seperately.
>
> ; Temperature coupling =
> tcoupl = no
> Pcoupl = no
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel = no
> gen_temp = 320
> gen_seed = 473529
>
> ; OPTIONS FOR BONDS =
> ; MARTINI - for ring systems constraints are defined
> ; which are best handled using Lincs.
>
> constraints = none
> ; Type of constraint algorithm =
> constraint_algorithm = Lincs
> ; Do not constrain the start configuration =
> unconstrained_start = no
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs_order = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs_warnangle = 30
>
>
>
> On Tue, Sep 29, 2009 at 4:17 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> sunny mishra wrote:
>
> Hi,
>
> I have a quick question. My system exploded when I tried to run
> the simulation and it gives me the LINCS warning. I am using
> MARTINI forcefield and finally I get segmentation fault. I don't
> know that what are the factors do i need to change to get rid of
> the LINCS warning. Please let me know. I also tried changing the
> large Van Der Waal distance but it doesn't work either. Do you
> have any idea?
>
>
> General answer: your system is unstable. Changing cutoffs
> haphazardly is a recipe for failure; these values are often
> intimately linked to the validity of the force field. You will
> probably have to provide more information on what you are doing
> (system description, as well as your .mdp file). Now that the
> mailing list search is functioning again (officially), you should be
> able to search the list archive. LINCS errors are posted weekly, if
> not daily sometimes!
>
> -Justin
>
> Sunny
>
>
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>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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