On 8/15/15 9:51 AM, anu chandra wrote:
Dear Gromcas users,
I have used grompp, as shown below, to generate .tpr file in order to
continue the simulation.
gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
index.ndx -p topol.top
My mdp input parameters are shown below,
***************************************************************
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 2500000
nstlog = 1000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy = 100
nstenergy = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps = PROT NPROT SOL_ION
tau_t = 1.0 1.0 1.0
ref_t = 303.15 303.15 303.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
gen-vel = no
;
nstcomm = 100
comm_mode = linear
comm_grps = PROT NPROT SOL_ION
;
refcoord_scaling = com
*******************************************************************
Unfortunately log file shows simulation time as a new start, not as
continuation from previous run, as shown below. Time suppose to start from
10001 ps.
******************************************************************************************
Started mdrun on rank 0 Sat Aug 15 13:15:04 2015
Step *Time* Lambda
0 *0.00000 * 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
2.70981e+04 1.28824e+05 9.76982e+04 2.20959e+03 2.96128e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
1.93530e+04 -3.84842e+04 7.57381e+04 -1.87856e+06 7.47371e+03
Position Rest. Dih. Rest. Potential Kinetic En. Total Energy
1.93759e+03 0.00000e+00 -1.55642e+06 4.40783e+05 -1.11564e+06
Temperature Pressure (bar) Constr. rmsd
3.03457e+02 2.41812e+02 3.91153e-06
DD step 24 load imb.: force 21.2% pme mesh/force 0.689
At step 25 the performance loss due to force load imbalance is 9.0 %
NOTE: Turning on dynamic load balancing
DD step 999 vol min/aver 0.816 load imb.: force 1.5% pme mesh/force
0.768
Step *Time* Lambda
1000 *2.00000* 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
2.70890e+04 1.29741e+05 9.79287e+04 2.28826e+03 2.58526e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
1.94561e+04 -3.80345e+04 7.15659e+04 -1.87484e+06 7.69793e+03
Position Rest. Dih. Rest. Potential Kinetic En. Total Energy
2.00424e+03 0.00000e+00 -1.55485e+06 4.41080e+05 -1.11377e+06
Temperature Pressure (bar) Constr. rmsd
3.03661e+02 1.71385e+02 3.91311e-06
*************************************************************************************************
Can any body help me to figure this out?
If you continue via grompp, you need to set tinit and init_step to get
continuous output. Continuing via the convert-tpr/mdrun -cpi approach will
continue seamlessly. If you have provided all of the correct inputs to grompp,
the physics is fine; you just need to post-process when concatenating the
trajectories (trjcat -settime).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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