On 12/11/12 8:45 AM, Shima Arasteh wrote:
Dears,
I am trying to simulate a system of water, POPC and protein using charmm36 ff.
I follow the protocol suggested in KALP15-DPPC tutorial.
I follow the tutorial step by step up to NVT equilibration without any bond or
any other type warnings.
Then I run the grompp :
# grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
My nvt.mdp file is as :
define = -DPOSRES
; Parameters describing the details of the NVT simulation protocol
integrator = md
dt = 0.002
nsteps = 50000
; Parameters controlling output writing
nstxout = 1000
nstvout = 1000
nstenergy = 1000
nstlog = 1000
; Parameters describing neighbors searching and details about interaction
calculations
ns_type = grid
nstlist = 5
rlist = 1.2
rlistlong = 1.4
rcoulomb = 1.2
rvdw = 1.2
pbc = xyz
Note that you should be using a switch potential for vdW interactions:
http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
; Parameters for treating bonded interactions
continuation = no
constraint_algorithm = LINCS
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Parameters for treating electrostatic interactions
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling parameters
tcoupl = v-rescale
tc-grps = Protein POPC SOL_CL ; Define groups to be coupled
separately to temperature bath
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
; Pressure coupling parameters
pcoupl = no
; Miscellaneous control parameters
; Dispersion correction
DispCorr = EnerPres
; Initial Velocity Generation
gen_vel = yes
gen_temp = 310
gen_seed = -1
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm = 1
comm_mode = Linear
comm_grps = Protein_POPC SOL_CL
# mdrun -deffnm nvt -v
In this step, the nvt is not done and what I get is as :
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 4707 and 4716 at distance 3.491 which is
larger than the 1-4 table size 2.200 nm
The fact that NVT fails immediately (i.e. at step zero) indicates that energy
minimization did not reach a sufficiently low value of Fmax. You probably have
unresolved clashes in the system.
-Justin
--
========================================
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
========================================
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