Dear All,
I am able to write the trajectory of a minimization of a peptide salvated
in TIP3PBOX. I have used this .in file
&cntrl
imin=1,
maxcyc=20000,
ncyc=4000,
cut=10.0,
ntb=1,
ntr=0,
ntpr=100,
ntwx=100,
ioutfm=1,
/
Then I calculate the rmsd to the first frame using ptraj and whith:
trajin ./min.mdcrd
rms first out rmsd_to_first.dat .N,CA,C
and I get a very nice plot showing how the peptide converges to a local
minimum and does not change noticeable any more. However, I cannot get
sander nor sander.MPI to write the trajectory file if I use generalized
Born implicit solvent. In that case I use:
&cntrl
imin=1,
maxcyc=2000,
ncyc=1000,
cut=999.,
rgbmax=999.,
igb=1,
ntb=0,
ntpr=50,
ntwx=50,
ioutfm=1,
/
and I am setting approppriatelly -i -o -p -c -r -x.
Do you know how can I get the trajectory when using generalized Born
implicit solvent? I only found a very old similar post (
http://archive.ambermd.org/200502/0076.html) but is not really helpful.
Thanks,
Edwin.
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Received on Wed Mar 18 2015 - 10:00:04 PDT
