[gmx-users] extending simulation with grompp incorporating velocities

[Chandan Choudhury]

On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
>
>>
>> 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
>>
>
> Use tpbconv -extend. See http://www.gromacs.org/**Documentation/How-tos/**
> Extending_Simulations<http://www.gromacs.org/Documentation/How-tos/Extending_Simulations>


I was aware with the tpbconv command. But while using the tpbconv command,
we cannot change the output frequency. If somehow the trajectory writing
frequency can be changed, it will solve my curiosity.

Chandan



>
>
>  ; 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.
>>
>
> On the information given, I can't explain this observation.
>
> Mark
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