Da-Wei Li wrote:
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3. This
is a test case only and the protein is 1UBQ. Grompp wills top for about
10 minutes then go through.
The efficiency of this kind of process will depend on the amount of available
memory on the system. You're asking grompp to decouple a huge amount of degrees
of freedom, which will require a lot of memory to do. It sounds like it's
working, in any case, so there's no real problem.
Whether or not simultaneously decoupling the LJ and Coulombic interactions of a
whole protein will generate a stable trajectory or sensible result is another
matter.
-Justin
***********output of grompp*****************
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Coupling 1 copies of molecule type 'Protein'
Setting gen_seed to 8552
Velocities were taken from a Maxwell distribution at 300 K
********************************
Command line and mdp file:
******************************
grompp -f pr1.mdp -c after_em.gro -t em.trr -p topol.top -o pr1
******************************
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = sd ; leap-frog integrator
nsteps = 5000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 5000 ; save velocities every 100ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = hbonds ; H bonds constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 20 fs
rlist = 0.8 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; 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 = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
;free energy stuff
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3
couple-moltype = Protein
couple-lambda0 = vdw-q
couple-lambda1 = none
*******************************
thanks.
dawei
On Mon, Feb 7, 2011 at 1:05 PM, TJ Mustard <musta...@onid.orst.edu
<mailto:musta...@onid.orst.edu>> wrote:
Dawei,
I have no problems with proteins in the thousands of atoms. Can you
post your command line and mdp files?
Thank you,
TJ Mustard
On February 7, 2011 at 9:31 AM Da-Wei Li <lida...@gmail.com
<mailto:lida...@gmail.com>> wrote:
Well. It actually isn't dead but becomes very slow for large
proteins. dawei
On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li <lida...@gmail.com
<mailto:lida...@gmail.com>> wrote:
hi,
I did more test and found that it depended on size of the
protein. Grompp will die when number of atoms of the protein
is larger than about 200. Is it possible the source code limit
the size of the protein that can be decoupled?
thanks.
dawei
On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li <lida...@gmail.com
<mailto:lida...@gmail.com>> wrote:
Dear users
I tried free energy calculation but grompp couldn't go
through. It stops after
*******************
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning H bonds into constraints...
Coupling 1 copies of molecule type 'Protein'
*******************
The CPU usage is 100%.
I just add following into the mdp file:
***************
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3
couple-moltype = Protein
couple-lambda0 = vdw-q
couple-lambda1 = none
***************
Does anyone have some idea about this problem? thanks.
Another question is whether I can switch off "two
molecules" (such as protein+ligand) in free energy
calculation? I searched this list and got that 4.0.7 did
support this. how about 4.5.4?
dawei
TJ Mustard
Email: musta...@onid.orst.edu <mailto:musta...@onid.orst.edu>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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