[AMBER] vacuum simulation fails using pmemd

From: g t <sketchfoot.gmail.com>
Date: Fri, 22 Jun 2012 12:12:04 +0100

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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Received on Fri Jun 22 2012 - 04:30:03 PDT
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