Dear Amber users,
I want to restart and SMD simulation with Amber12.
Below are the first input file, which I launched with the -O option of
sander
SMD
&cntrl
imin = 0, irest = 0, ntx = 1,
ntt = 3, gamma_ln = 5.0,
tempi = 310.0, temp0 = 310.0,
pres0 = 1.0, ntp = 1, taup = 2.0,
ntb = 2, ntc = 2, ntf = 2,
cut = 8, ntr = 0,
ntpr = 5000, ntwx = 10000, ntwr = 10000, ntwv = 0,
ioutfm = 1,
iwrap = 0,
nstlim = 2000000, dt = 0.002, nrespa = 1, ig = -1,
jar = 1
/
&wt type='DUMPFREQ', istep1=100 /
&wt type='END' /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
and here is the restart input file, which I launched with the -A option,
that should be used in conjunction with irest=1 for restarting simulation
and appending to existing files:
&cntrl
imin = 0, *irest = 1, ntx = 5*,
ntt = 3, gamma_ln = 5.0,
temp0 = 310.0,
pres0 = 1.0, ntp = 1, taup = 2.0,
ntb = 2, ntc = 2, ntf = 2,
cut = 8, ntr = 0,
ntpr = 5000, ntwx = 10000, ntwr = 10000, ntwv = 0,
ioutfm = 1,
iwrap = 0,
nstlim = 2000000, dt = 0.002, nrespa = 1,
jar = 1
/
&wt type='DUMPFREQ', istep1=100 /
&wt type='END' /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
Now, while the mdinfo and trajectory files are updated by appending the new
information,
the mdout and dist_vs_t files are not.
Thus my question is if I am doing something wrong with the inputs or if I
have to rename out and DUMPAVE files in every run.
Thanks a lot,
Attilio
--
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Attilio Vittorio Vargiu, PhD
SLACS & Department of Physics, University of Cagliari
Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700
09042 Monserrato (CA), Italy
e-mail1: vargiu.dsf.unica.it
e-mail2: attilio.vargiu.gmail.com
Phone: +390706754847
Fax: +39070510171
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Received on Tue Mar 12 2013 - 09:00:02 PDT
