On 3/24/14, 7:48 AM, Ankita Naithani wrote:
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 25 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
cutoff-scheme = Verlet
But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter
file.
That option was introduced in version 4.6. It won't work with an earlier
version.
-Justin
On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar <kumar.pavan...@gmail.com>wrote:
Hello Ankita
You have to just include the following line in your mdp file
cutoff-scheme=Verlet
And run your grompp with the modfied mdp file to generate tpr file and then
mdrun.
Hope this doesn't give you the same error
On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
<ankitanaith...@gmail.com>wrote:
Hi,
I am trying to run a simulation of my protein (monomer ~500 residues). I
had few questions and erors regarding the same.
I have previously run the simulation of the apo form of the same protein
using Gromacs 4.5.5 which was available at the cluster facility I was
using
and also which is installed in my system. However, when I tried to run
the
holo form, I got error :
Fatal error:
11 particles communicated to PME node 106 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
This I figured out could be solved using a lower timestep as my previous
timestep was 4fs and now I have reduced it to 3fs which should work fine
now.
However, after producing the tpr file for production run in my GROMACS
4.5.5, I realised that the grant for the cluster facility is over and the
new clusters which I am trying to set up the same protein for support
only
gromacs 4.6. I am trying to run the code in these clusters and I get he
following error:
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.6.3
Source code file: /home/gromacs-4.6.3/src/kernel/runner
.c, line: 824
Fatal error:
OpenMP threads have been requested with cut-off scheme Group, but these
are
only
supported with cut-off scheme Verlet
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
---------------------------------------------------------------------------------
1. I wanted help with my mdp options to make it compatible.
2. Since my pevious calculations were based on gromacs 4.5.5, switching
to
gromacs 4.6, would that break the continuity of the run or would that
bring
about differences in the way the trajectories would be analysed?
Below, is my mdp file
title = production MD
; Run parameters
integrator = md ; leap-frog algorithm
nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n
dt = 0.003 ; 3 fs
; Output control
nstxout = 0 ; save coordinates every 2 ps
nstvout = 0 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps
nstenergy = 1000 ; save energies every 5 ps
nstlog = 1000 ; update log file every 5 ps
energygrps = Protein ATP
; Bond parameters
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 25 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
nstcomm = 10 ; remove com every 10 steps
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 318 318 ; reference temperature, one for each
group,
in K
; Pressure coupling is off
pcoupl = berendsen ; Berendsen thermostat
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 1.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; Velocity generation is on
gen_temp = 318 ; reference temperature, for protein in K
Kind regards--
Ankita Naithani
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Pavan
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