Dear AmberGurus,
I'm running (i think) an accelerated MD run (a la page 158 of amber12.pdf.)
Essentially I'm attempting to look at an explicitly solvated protein
(TIP4Pew). paramaters were chosen based on the instructions in the manual,
the paper, and the equilibration MD run.
I ran a "test run" but found that although the mdcrd file (two runs, one
with ioutfm=1 and one with ioutfm=0) was populated, loading the files into
vmd yielded nothing.... sizewise the mdcrd file seems to be significantly
smaller (ioutfm=0) than the .rst file. I'm wondering, am I missing
something? Is the output from an aMD run different than a standard MD run?
Here is the input file I used for the test;
&cntrl
imin=0, irest=1, ntx=5,
dt=0.002, ntc=2, ntf=2, tol=0.000001,iwrap=1,
ntb=2, cut=12.0, ntp=1,igb=0,ntwprt = 3381,ioutfm = 1,
ntt=3, temp0=310.0, gamma_ln=1.0, ig=-1,
ntpr=1000, ntwx=1000, ntwr=1000, nstlim=2000000,
iamd=3,EthreshD=25120,
alphaD=787,EthreshP=-413156,
alphaP=34008,
/
&ewald
dsum_tol=0.000001,
/
Best,
JOnathan
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Received on Sun May 05 2013 - 06:00:03 PDT
