[gmx-users] Re: free energy calculation , grompp crash
Da-Wei Li
lidawei at gmail.com
Mon Feb 7 19:15:18 CET 2011
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.
***********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 <mustardt at 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 <lidawei at 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 <lidawei at 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 <lidawei at 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: mustardt at onid.orst.edu
>
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