Dear Amber 8 users,
I am experiencing problems with the restart of the MD simulation for my
small peptide, with water as the explicit solvent. Thus far, I was able
to perform 16600ps of the MD production run. However, from the next
cycle, ie 16900-17000ps, it complains about reading the box
information-(using amber8 on a 8 processor machine).-the input & output
files are attached. It seems like the box info is not being read? Any
suggestions on howto overcome this problem would be appreciated.
thank you,
vincent
Input file for MD
Production run at 300 K using PME
&cntrl
dt=0.002, imin = 0, scee=1.2,
cut = 10.0, temp0 = 300,
ntx = 7, irest = 1, tempi = 300,
ntf = 2, ntc = 2, tol = 0.0001,
ntb = 2, ntp = 1, npscal = 1, pres0 = 1.0, taup = 2.0,
nstlim =50000, GAMMA_LN = 1.0,
ntpr = 100, ntt = 3, ntwx = 100, ntwe = 100, ntwr=1000,
/
&ewald
skinnb = 1.0,
/
output file
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 10/28/2004 at 14:02:01
[-O]verwriting output
File Assignments:
| MDIN: boxpmedyn.in1
| MDOUT: out16900a17000ps.out
|INPCRD: 1085.rst
| PARM: metenkf.top
|RESTRT: 1086.rst
| REFC: 1085.rst
| MDVEL: mdvel
| MDEN: en16900a17000ps
| MDCRD: crd16900to17000ps
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
equilibration at 300 K using PME
"out16900a17000ps.out" 47 lines, 2772 characters
/
&ewald
skinnb = 1.0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: SGIFFT MPI
getting new box info from bottom of inpcrd
Dr K Bisetty
Senior Lecturer
Department of Chemistry
Steve Biko Campus
Durban Institute of Technology
P O BOX 1334
Durban
4000
Tel : +27-031-2042311
Fax : +27-031-2022671
"ND-4-SPD"
bisettyk.dit.ac.za
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Received on Thu Oct 28 2004 - 15:53:01 PDT
