Dear all,
When I used the pmemd.cuda(version 14) to run aMD simulation.
The error occurred and could you tell me how to fix it ?
Thx
YT
aMD.in
----------------------------------------
[c00jsw00.james35 prion]$ more amd.in
500 ps NVT production
NVT
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000000,dt=0.002,
ntc=2,ntf=2,ig=-1,
cut=10.0, ntb=1, ntp=0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,ioutfm=1,
iamd=3,iwrap=1,
pdhgt=1830.00,
pdtune=83.20,pdhgta=-56599.00,
pdtunea=3060.00,
/
amd.out
------------------------------------------------------
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
500 ps NVT production
NVT
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000000,dt=0.002,
ntc=2,ntf=2,ig=-1,
cut=10.0, ntb=1, ntp=0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,ioutfm=1,
iamd=3,iwrap=1,
pdhgt=1830.00,
pdtune=83.20,pdhgta=-56599.00,
pdtunea=3060.00,
/
Note: ig = -1. Setting random seed to 4034 based on wallclock time in
microseconds.
| Using Accelerated MD (AMD) RASING VALLEYS to enhance sampling iamd = 3
| AMD boost to total energy: EthreshP,alphaP 0.000000000000
0.000000000000
| AMD boost to dihedrals: EthreshD,alphaD 0.000000000000
0.000000000000
| AMD error all main parameters are 0.0 for Accelerated MD (AMD) or
Windowed Accelerated MD (wAMD)
Input errors occurred. Terminating execution.
error
----------------------------------------
[c00jsw00.james35 prion]$ pmemd.cuda -O -i amd.in -o amd.out -p w.top -c
eq.rst -r amd.rst
Cannot match namelist object name pdhgt
namelist read: misplaced = sign
Cannot match namelist object name 830.00
Cannot match namelist object name pdtune
namelist read: misplaced = sign
Cannot match namelist object name 3.20pdhgta
namelist read: misplaced = sign
Cannot match namelist object name 56599.00
Cannot match namelist object name pdtunea
namelist read: misplaced = sign
Cannot match namelist object name 060.00
STOP PMEMD Terminated Abnormally!
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Received on Sun Oct 12 2014 - 07:30:02 PDT
