Dear AMBER users,
I'm currently trying to run my systems using AMBER, but got a problem
when I'm trying to restart the simulation from previous run. What I did
is simply copy the restrt file with coordinations and velocities, then
restart the job. But when I check the output data in the .mdout file and
found the data at the same time point are obviously different from
previous run. I'm showing the output data below,
output from previous run:
------------------------------------------------------------------------------
NSTEP = 19100 TIME(PS) = 19.100 TEMP(K) = 310.64 PRESS =
108.3
Etot = -115443.8315 EKtot = 63808.8852 EPtot =
-179252.7167
BOND = 6427.0827 ANGLE = 20861.9145 DIHED =
19312.3654
1-4 NB = 7667.1271 1-4 EEL = 45965.9718 VDWAALS =
-2041.0234
EELEC = -283272.0143 EHBOND = 0.0000 RESTRAINT =
5825.8596
EAMBER (non-restraint) = -185078.5763
EKCMT = 15177.8128 VIRIAL = 12358.3086 VOLUME =
1205411.4892
Density =
0.7793
Ewald error estimate: 0.7667E-05
------------------------------------------------------------------------------
output from restart run:
------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 19.100 TEMP(K) = 2577.07 PRESS =
3038.9
Etot = 1186017.0983 EKtot = 529351.1325 EPtot =
656665.9659
BOND = 61421.6074 ANGLE = 144578.4722 DIHED =
35952.4406
1-4 NB = 25241.3256 1-4 EEL = 45008.7399 VDWAALS =
17408.1792
EELEC = -268207.1839 EHBOND = 0.0000 RESTRAINT =
595262.3848
EAMBER (non-restraint) = 61403.5811
EKCMT = 46647.5543 VIRIAL = -34506.8870 VOLUME =
1236836.9095
Density =
0.7595
Ewald error estimate: 0.5371E-05
------------------------------------------------------------------------------
My .mdin file for previous run:
&cntrl
imin=0,irest=0,ntx=1,
cut=12.0,scee=1.2,
tempi=310.0,temp0=310.0,
ntt=3,gamma_ln=1.0,
ntp=2,pres0=1.0,taup=2.5,
vlimit=25.0,
ntb=2,ntc=2,ntf=2,
nstlim=500000,
iwrap=1,
ntwe=100,ntwx=1000,ntpr=100,
ntr=1,
&end
GRP1
100.0
ATOM 1 13609
END
END
My .mdin file for restart run:
&cntrl
imin=0,irest=1,ntx=5,
cut=12.0,scee=1.2,
tempi=310.0,temp0=310.0,
ntt=3,gamma_ln=1.0,
ntp=2,pres0=1.0,taup=2.5,
vlimit=25.0,
ntb=2,ntc=2,ntf=2,
nstlim=500000,
iwrap=1,
ntwe=100,ntwx=1000,ntpr=100,
ntr=1,
&end
GRP1
100.0
ATOM 1 13609
END
END
It's really weird that the restart is so different and even crash. I
know I might need change some better control parameters in .mdin, even
so, the restarted simulation should be continuous with previous run. Any
suggestion will be really appreciated! Have a nice weekend!
Kefa
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Received on Wed Aug 19 2009 - 22:36:38 PDT
