Hi,
On Wed, Mar 18, 2015 at 10:41 AM, Edwin Helbert Aponte Angarita
<helbert2a.gmail.com> wrote:
> 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:
Do you get any output at all (i.e. in your mdout or mdinfo files)? Are
your GB simulations completing without error?
-Dan
>
> &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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 18 2015 - 20:00:02 PDT
