Hi David,
Le 16 déc. 2019 à 12:15, David Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> a écrit :
On Mon, Dec 16, 2019, Jerome Eberhardt wrote:
I tried to use igb = 6 with imin = 5, it does not work neither and if I
do the minimization with imin = 1 and igb = 6, it gives me a completely
different result at the end, with a positive final energy.
I'm a bit lost here: you show results for imin=1/igb=0/ntb=0, and for
imin=5/igb=0/ntb=0. I would have expected these to be the same, but
there may well be some bug here. Are both the prmtop file and all the
rst7 files non-periodic? I ask because you see to have WAT residues in
your system....
Yes, it is confusing I know. I do have WAT residues in my system. But the system is non-periodic because I didn’t produce them using MD simulations. Although, there was some periodic information in the rst7 file, but even if I remove that information sander still complain about the virtual box.
You say above that imin=5/igb=6/ntb=? does not work, but it would be
very helpful to see what the error is there.
With imin=5, igb=6, ntb=0, cut=999 this is the error that I get on one frame:
### OUTPUT ###
minimizing coord set # 1
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
31 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 402061.1644 DIHED = 1824.1160
VDWAALS = 0.0000 EEL = 0.0000 EGB = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
EAMBER = NaN
minimization completed, ENE= NaN RMS= NaN
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.
##############
command line: sander -O -i min.inp -o min.out -p protein_system.prmtop -c protein_system.rst7 -ref protein_system.rst7 -x protein_system-test.rst7 -y protein_system.rst7
You are exploring a corner case here: trying to apply a vacuum energy
function to a protein system is pretty unusual these days, and this
capability may have stopped working at some point. But using igb=6 (and
not igb=0) is definitely the way to go. (Setting igb=6 avoids the
formation of a "virtual box" and all its problems.)
Ok, I will start playing with igb=6 instead of igb=0.
Thanks!
Jerome
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:
AMBER.ambermd.org>
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 16 2019 - 17:00:02 PST
