Dear Amber users,
When analysing my output files with the script “process_mdout.perl”, I find that it is not retrieving the density, nor the volume, of my system as both summary.DENSITY and summary.VOLUME files only contain the time elapsed. Am I using an “old” version? You can find it in attachements.
This is the input that produces the output file I’m trying to analyse:
Constant Temp 300K Pres 1.0 MD
&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=2.0,
nstlim=50000, dt=0.001,
ntpr=500, ntwx=200, ntwr=10000,
ntc=2, ntf=2,
noshakemask = '.474-494,521-534,900-909,917-933,2646-2689,2828-2851,2931-2936’,
ntr=1,
restraintmask = ':170,185,.CA,C,N',
restraint_wt=5.0,
ifqnt=1,
/
&qmmm
qmmask=':32,35,59,61,168,169,179,186-187,1007,2332,2637',
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qmcut=12.0,
/
Thanks for any help!
Ruth
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Received on Tue Jun 21 2016 - 09:00:03 PDT
