Thanks Jason, I will try as you suggest. :)
best regards,
gt
On 22 June 2012 16:14, Jason Swails <jason.swails.gmail.com> wrote:
> pmemd does not explicitly support vacuum simulations. I think I recall a
> thread in the past that you can hijack GB to give you vacuum results if you
> set the external dielectric constant to 1, but you should run a quick
> simulation with vacuum in sander to verify this statement is true.
>
> Also, if you really want vacuum simulations, I strongly suggest you think
> about using an infinite cutoff for non-bonded interactions (your output
> file suggests that you are using a value of 10). Short cutoffs of this
> magnitude are really only sensible for PME simulations where there is no
> truncation of long range electrostatic interactions.
>
> HTH,
> Jason
>
> On Fri, Jun 22, 2012 at 7:12 AM, g t <sketchfoot.gmail.com> wrote:
>
> > Hi,
> >
> > I'm trying run a vacuum simulation on a small alcohol (hexan-1-ol). I
> have
> > managed to minimise and run a short equilibration phase. However, the
> > simulation fails to run in the production phase. I have periodic boundary
> > turned off and implicit water turned off. The error I get is the
> following:
> >
> > ########################
> >
> >
> > | PMEMD implementation of SANDER, Release 10
> >
> > | Run on 06/21/2012 at 22:40:52
> >
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: prod.in
> >
> > | MDOUT: md_1.out
> >
> > | INPCRD: ../cv/cv.rst
> >
> > | PARM: ../leap/hex_ligand_vac.parm
> >
> > | RESTRT: md_1.rst
> >
> > | REFC: ../cv/cv.rst
> >
> > | MDVEL: mdvel
> >
> > | MDEN: mden
> >
> > | MDCRD: md_1.crd
> >
> > | MDINFO: mdinfo
> >
> > |LOGFILE: logfile
> >
> >
> >
> > Here is the input file:
> >
> > Constant pressure constant temperature production run
> >
> > &cntrl
> >
> > nstlim=12500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000,
> ntwx=500,
> >
> > temp0=300.0, ntt=1, tautp=2.0, ig=-1, cut=10.0, igb=0,
> >
> >
> >
> > ntb=0, ntp=0,
> >
> >
> >
> > ntc=2, ntf=2,
> >
> >
> >
> > nrespa=1,
> >
> >
> >
> > ntr=1,
> >
> > &end
> >
> >
> >
> >
> > | INFO: Axis order optimization will be used.
> >
> > | ERROR: nfft1 must be in the range of 6 to 512!
> > | ERROR: nfft2 must be in the range of 6 to 512!
> > | ERROR: nfft3 must be in the range of 6 to 512!
> > | ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
> > | ERROR: b must be in the range of 0.10000E+01 to 0.10000E+04!
> > | ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
> > | ERROR: fft_blk_y_divisor must be in the range of 2 to
> 1!
> >
> > Input errors occurred. Terminating execution.
> >
> > ####################################################
> > ####################################################
> >
> > My input files for minimisation and equilibration are listed below:
> > #####################
> > Minimisation:
> > &cntrl
> > imin=1, ntmin=1, maxcyc=100000, ncyc=1500,
> > ntb=0, ntpr=5, ntwr=1000, drms=0.05, igb=0,
> > cut=9999.0,
> > /
> > ######################
> >
> > equilibration stage 1
> > &cntrl
> > nstlim=60000, dt=0.002, ntx=1, irest=0, ntpr=250, ntwr=500, ntwx=50,
> > tempi=100.0, temp0=300.0, ntt=1, tautp=2.0, ig=-1, igb=0,
> >
> > ntb=0, ntp=0,
> >
> > ntc=2, ntf=2,
> >
> > nrespa=2, cut=10.0,
> > &end
> >
> > Any help anyone could offer would be greatly appreciated.
> >
> > Best regards,
> > GT
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 23 2012 - 11:00:02 PDT
