Restarting file does not generate - 12/12/19 05:28 AM

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

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