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Restarting file does not generate
#37783 12/12/19 05:28 AM
Joined: Oct 2019
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vht Offline OP
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Joined: Oct 2019
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Hi all,

The following command was given to generate the restart file for the MD simulation, comnew-equil-1.res.


open unit 41 write card name comnew-equil-1.res !restart file that will be written
open unit 51 read card name comnew-heat.res !restart file that will be reading
open unit 31 write file name comnew-equil-1.dcd !trajectory file name

! set up nonbond parameters -- same as for heating
nbond inbfrq -1 imgfrq -1 atom vatom cdie eps 1.0 -
elec ewald pmew fftx 48 ffty 48 fftz 48 kappa .34 spline order 6 -
vdw vswitch cutnb 16.0 cutim 16.0 ctofnb 12. ctonnb 10. wmin 1.0

! We're going to use the Langevin piston method, so we're going to need to
! calculate masses for the pressure and temperature pistons (pmass & tmass)
! calc pmass = total molecular mass / 50
! calc tmass = pmass * 10
scalar mass stat
calc pmass = int ( ?stot / 50.0 )
calc tmass = @pmass * 10

dyna leap cpt restart - ! restart the run from our heating restart, use CPT dynamics
timestep 0.001 nstep 5000000 nprint 10000 - ! do 5000 picoseconds, 1 fs time steps
hoover reft 310.0 tmass @tmass - ! hoover thermostat, constant temp - 310 K, tmass as above
pcons pint pref 1.0 pmass @pmass pgamma 0.0 - ! constant pressure, 1 atmosphere, use internal virial (pint), collision freq. 0
ihtfrq 0 ieqfrq 0 ntrfrq 500 - ! temperature under Hoover's control, cancel rotation/translation every 10 steps
iunrea 51 iunwri 41 iuncrd 31 nsavcc 100 - ! units for reading/writing restarts and coordinate trajectory
iasors 1 iasvel 1 iscvel 0 ichecw 0 - ! since we're restarting and ihtfrq = ieqfrq = 0, these don't really matter
echeck 100. ! check energy diff as before

This simulation is running in the cluster therefore needs to restart every 24 hours but nothing was written in the comnew-equil-1.res.

Any help is greatly appreciated.

Thanks.
VH

Re: Restarting file does not generate
vht #37784 12/12/19 10:25 AM
Joined: Sep 2003
Posts: 4,762
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The restart file is written at the end of the run. Reduce NSTEP so that the run ends within 24 hours.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  John Legato, lennart 

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