[gmx-users] LINCS dependence
sunny mishra
mishra.sunny at gmail.com
Tue Sep 29 22:55:42 CEST 2009
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.
;
; 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> 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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>
> --
> ========================================
>
> 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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