[gmx-users] extending simulation with grompp incorporating velocities

[Chandan Choudhury]

Dear gmx users,

A simulation was performed for 50 ns with

; RUN CONTROL
integrator               = md
nsteps                   = 50000000
dt                       = 0.001
; OUTPUT CONTROL
nstxout                  = 1000
nstvout                  = 1000
nstxtcout                = 0
nstlog                   = 100
nstenergy                = 100

The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt,
state_prev.cpt. The simulation completed normally.

After 50 ns, I intend to extend for 4 more ns, write the trajectory file
frequently with
; RUN CONTROL
integrator               = md
nsteps                   = 4000000
dt                       = 0.001
; OUTPUT CONTROL
nstxout                  = 00
nstvout                  = 00
nstxtcout                = 10
nstlog                   = 500
nstenergy                = 10

$grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb  -n index.ndx

$gmxdump -s md50-54.tpr | more

md50-54.tpr:
inputrec:
   integrator           = md
   nsteps               = 4000000
   init_step            = 0
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 1
   comm_mode            = Linear
   nstlog               = 500
   nstxout              = 0
   nstvout              = 0
   nstfout              = 0
   nstenergy            = 10
   nstxtcout            = 10
   init_t               = 0
   delta_t              = 0.001
   xtcprec              = 1000
   nkx                  = 22
   nky                  = 22
   nkz                  = 40
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bPeriodicMols        = FALSE
   bContinuation        = FALSE
   bShakeSOR            = FALSE
   etc                  = V-rescale
   epc                  = Berendsen
   epctype              = Isotropic
   tau_p                = 1

$mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr -g
50-54.log -cpi state.cpt -nice 0

state.cpt is the output of the initial 50ns run. I have used state.cpt to
incorporate the velocities frm the initial run.
So, I would expect my 2nd simulation to get complete after running for 4 ns.
But, that was not the case. I have checked the log file. The time clearly
exceeds 4ns.

$ tail -15 50-54.log
DD  step 54500989 load imb.: force  5.6%  pme mesh/force 0.429

DD  step 54500999 load imb.: force  6.0%  pme mesh/force 0.428

           Step           Time         Lambda
       54501000    54501.00259        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    1.82780e+02    3.37147e+02    8.77788e+01    1.92877e+01    3.90071e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    5.96624e+02    7.91553e+04   -5.73437e+05   -2.73830e+04   -5.20402e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    9.75908e+04   -4.22811e+05    2.97855e+02   -5.82198e+01

Kindly suggest what wrong am I doing. and how do I incorporate the velocity
from my earlier run.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111021/a3d84b55/attachment.html>