On 11/16/12 10:10 AM, Kavyashree M wrote:
Hi Ananya,
Can you try with rvwd 0.9nm and rcolumb with 1.4nm..?
vdw interaction decreases as 1/r^6, while columbic
interaction decreases as (1/r).. so it would be better if
you consider columbic interaction for longer distance
than vdw interaction..
One should not make haphazard changes to cutoffs. They are part of the force
field. Changing them without basis can invalidate the force field model.
-Justin
bye
kavya
On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee <
ananyachatter...@iiserkol.ac.in> wrote:
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 <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.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
<htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
<http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
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.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
