Hi all,
As suggested by venhat I have energy minimised it till 1000Kj/mol but
even now I am getting the same error, saying
Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
t = 90.674 ps: Water molecule starting at atom 236548 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/mdlib/nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
can anyone suggest me what to do now.
Ananya Chatterejee
On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote:
I think the system is not well energy minimized. Do it for
1000kj/mol. Also
check for bad contacts in your starting structure using Ramachandran
plot.
One more important thing is that, you have to generate an index file
with
Protein_GTP as one group and water_Ions as another. Then change your
tc-groups as
tc-grps = Protein_GTP Water_Ions
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300
On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee <
ananyachatter...@iiserkol.ac.in> wrote:
Hi all,
I was running a md simulation of protein complexed with GTP in
water,
neutralised with Mg2+ and Cl- ions.I have also em the system to
2000kj/mol
and also equilibrated the water molecules in 300K temperature and 1
bar
pressure. And then run the md simulation using md parameters as
follow:
title = Protein-ligand complex
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 5000000 = 1000 ps (1 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1ps
nstvout = 500 ; save coordinates every 1ps
nstenergy = 500 ; save energies every 1 ps
nstlog = 500 ; update log file every 1 ps
nstxtcout = 500 ; write .xtc trajectory every 1 ps
energygrps = Protein GTP SOL MG2+
; Bond parameters
constraints = none ; No constrains
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Temperature coupling
tcoupl = v-rescale ; modified Berendsen
thermostat
tc-grps = Protein GTP SOL MG2+ CL- ; two coupling groups
- more
accurate
tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps
ref_t = 300 300 300 300 300 ; reference
temperature, one
for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is
on for
NPT
pcoupltype = isotropic ; uniform scaling of box
vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in
bar
compressibility = 4.5e-5 ; isothermal
compressibility
of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
Now I am getting the following error.
Warning: 1-4 interaction between 3231 and 3234 at distance 10.730
which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
t = 226.610 ps: Water molecule starting at atom 236548 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
------------------------------**-------------------------
Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
kindly help me I am not getting where I am getting wrong.
--
Ananya Chatterjee,
Senior Research Fellow (SRF),
Department of biological Science,
IISER-Kolkata.
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--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
--
Ananya Chatterjee,
Department of biological Science,
IISER-Kolkata.
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