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
> _______________________________________________
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> 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
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Received on Fri Jun 22 2012 - 08:30:03 PDT
