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 <[email protected]
<mailto:[email protected]>> 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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
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Please search the archive at http://www.gromacs.org/search before
posting!
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interface or send it to [email protected]
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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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