When I do constant pressure after the heating step, the following error is reported:

ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values.

Your system density has likely changed by a large amount, probably from

starting the simulation from a structure a long way from equilibrium.

[Although this error can also occur if the simulation has blown up for some reason]

The GPU code does not automatically reorganize grid cells and thus you

will need to restart the calculation from the previous restart file.

This will generate new grid cells and allow the calculation to continue.

It may be necessary to repeat this restarting multiple times if your system

is a long way from an equilibrated density.

Alternatively you can run with the CPU code until the density has converged

and then switch back to the GPU code.

My system is protein and two ligand small molecules, cubic water box added by the tleap process, 12 Å, subsequent cut values set to 12 Å.

where the heat.in file is:

&cntrl

imin=0

irest=0,

ntx=1

nstlim=25000, dt=0.002,

ntc=2, ntf=2,

cut=12.0, ntb=1, ntp=0,

ntpr=500, ntwr=500, ntwx=500,

ntr=1, restraint_wt=25.0, restraintmask=':1-359',

ntt=3, gamma_ln=2.0, ig=-1, iwrap=1

tempi=0.0,

nmropt=1,

/

&wt type='TEMP0', istep1=0, istep2=25000,value1=0.0, value2=50.0, /

&wt type='END' /

where the density.in file is:

&cntrl

imin=0,irest=1,ntx=5,

nstlim=500000,dt=0.002,

ntc=2,ntf=2,

cut=12.0, ntb=2, ntp=1, pres0=1.0, taup=1.0,

ntpr=5000, ntwr=5000, ntwx=5000,

ntt=3, gamma_ln=2.0,

temp0=300.0, ig=-1, iwrap=1,

ntr=1, restraint_wt=25.0, restraintmask=':1-359',

nmropt=1,

/

&wt type='TEMP0', istep1=0, istep2=125000,value1=50.0, value2=300.0 /

&wt type='TEMP0', istep1=125001, istep2=500000,value1=300.0, value2=300.0 /

&wt type='END' /

Please help me. Thank you!

More Xiaoyan Yang's questions See All
Similar questions and discussions