On Fri, Jul 05, 2013, kirtana S wrote:
> source leaprc.ff03
> loadamberparams methanol.frcmod
> loadoff methanol.off
>
> setbox a vdw 2
> saveamberparm a M.prmtop M.inpcrd
>
> The library file, prmtop and inpcrd file are attached.
>
> My simulation run is minimization, constant volume simulations where I heat
> to 300K followed with constant pressure run
>
> &cntrl
> imin=0,
> ntxo=1, ntrx=1,
> cut=12.0,tempi=0.1,
^^^^^^^^^ way too big: use 8 or 9 Ang. here
> dt=0.002,dielc=33,
^^^^^^^^^^ wrong (bug I think it is ignored)
> ntc=2, ntf=2,tol=0.00001,
> ntx=1, irest=0,
> ntb=1,tautp=2,
> ntt=1,
> nmropt=1,ntr=1,
> /
> GROUP FOR CONSTRAINTS
> 0.5
> RES 1 1743
> END
> END
?? Why are you using constraints? What are residues 1 to 1743? It looks like
you have only 250 methanol molecules here.
>
> &cntrl
> imin=0,
> ntxo=1, ntrx=1,
> cut=12.0,tempi=300.0,
> ntpr=500, ntwx=500, ntwe=500,
> nstlim=500000, temp0=300.0,
> dt=0.002,dielc=33,
> ntc=2, ntf=2, tol=0.00001,
> ntx=5, irest=1,
> ntb=1,tautp=1,
> ntt=1,
> /
All the input files you have listed above set ntb=1, so there is no constant
pressure (at least as shown here). Maybe visualizing your trajectories (after
imaging them with cpptraj or ptraj) will help you identify the problem.
As I remember(?) the original comment was that the box was expanding. That
might or might not be a problem, but all the simulations you are describing
here would have constant volume, as far as I can see.
...good luck...dac
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Received on Fri Jul 05 2013 - 19:30:01 PDT
