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!