Dear Amber Users,
I perform a constant volume run and then do constant pressure , I forgot to
send the script related to constant pressure run
&cntrl
imin=0, ntx=5,
irest=1, ntxo=1,tempi=300.0,
ntf=2, ntc=2,cut=10.0,
ntpr=1000, ntwx=1000, ntwe=1000,
nstlim=5000000,tautp=2, temp0=300.0,
dt=0.002, nscm=100,taup=2,pres0=1,
igb=0,ntb=2,ntp=2,dielc=33,
ntt=1,
&end
Here in constant pressure run the box expands , decrease in density. Is it
possible to have experimental density of methanol.
I visualilzed trajectory after I image and center the residues using ptraj.
Thanks
Kirtana
On Fri, Jul 5, 2013 at 7:05 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 19:30:02 PDT
