Hi Justin,<br><br>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.<br>
<br>;<br>; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0<br>;<br>; for use with GROMACS 3.3<br>;<br><br>; VARIOUS PREPROCESSING OPTIONS = <br>title = Martini<br>cpp = /usr/bin/cpp<br><br>
; RUN CONTROL PARAMETERS = <br>; MARTINI - Most simulations are stable with dt=40 fs,<br>; some (especially rings) require 20-30 fs.<br>; The range of time steps used for parametrization <br>; is 20-40 fs, using smaller time steps is therefore not recommended.<br>
<br>integrator = steep<br>; start time and timestep in ps<br>tinit = 0.0<br>dt = 0.030<br>nsteps = 1000<br>; number of steps for center of mass motion removal = <br>
nstcomm = 1<br>comm-grps = <br><br>; OUTPUT CONTROL OPTIONS = <br>; Output frequency for coords (x), velocities (v) and forces (f) = <br>nstxout = 5000<br>nstvout = 5000<br>
nstfout = 0<br>; Output frequency for energies to log file and energy file = <br>nstlog = 1000<br>nstenergy = 1000<br>; Output frequency and precision for xtc file = <br>nstxtcout = 1000<br>
xtc_precision = 100<br>; This selects the subset of atoms for the xtc file. You can = <br>; select multiple groups. By default all atoms will be written. = <br>xtc-grps = <br>; Selection of energy groups = <br>
energygrps = <br><br>; NEIGHBORSEARCHING PARAMETERS = <br>; MARTINI - no need for more frequent updates <br>; or larger neighborlist cut-off due<br>; to the use of shifted potential energy functions.<br><br>
; nblist update frequency = <br>nstlist = 10<br>; ns algorithm (simple or grid) = <br>ns_type = grid<br>; Periodic boundary conditions: xyz or none = <br>pbc = xyz<br>
; nblist cut-off = <br>rlist = 1.2<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW = <br>; MARTINI - vdw and electrostatic interactions are used<br>; in their shifted forms. Changing to other types of<br>
; electrostatics will affect the general performance of<br>; the model.<br><br>; Method for doing electrostatics = <br>coulombtype = Shift <br>rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>
; Dielectric constant (DC) for cut-off or DC of reaction field = <br>epsilon_r = 15<br>; Method for doing Van der Waals = <br>vdw_type = Shift <br>; cut-off lengths = <br>rvdw_switch = 0.9<br>
rvdw = 1.2<br>; Apply long range dispersion corrections for Energy and Pressure = <br>DispCorr = No<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS = <br>; MARTINI - normal temperature and pressure coupling schemes <br>
; can be used. It is recommended to couple individual groups<br>; in your system seperately.<br><br>; Temperature coupling = <br>tcoupl = no<br>Pcoupl = no<br><br>; GENERATE VELOCITIES FOR STARTUP RUN = <br>
gen_vel = no<br>gen_temp = 320<br>gen_seed = 473529<br><br>; OPTIONS FOR BONDS = <br>; MARTINI - for ring systems constraints are defined<br>; which are best handled using Lincs. <br>
<br>constraints = none <br>; Type of constraint algorithm = <br>constraint_algorithm = Lincs<br>; Do not constrain the start configuration = <br>unconstrained_start = no<br>; Highest order in the expansion of the constraint coupling matrix = <br>
lincs_order = 4<br>; Lincs will write a warning to the stderr if in one step a bond = <br>; rotates over more degrees than = <br>lincs_warnangle = 30<br><br><br><br><div class="gmail_quote">On Tue, Sep 29, 2009 at 4:17 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
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?<br>
<br>
</blockquote>
<br></div>
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!<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Sunny<br>
<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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