Dear community,
In sander, it performs PME for calculation of electrostatic interaction in periodic system, and the 'cut' keyword is used only for the cutoff of direct space summation. Therefore, in principle, setting it as 8 Angstrom or 10 Angstrom won't significantly change the EEL energy in the output, this is also in a previous discussion at here RE: Re: [AMBER] cutoff from Ross Walker on 2010-06-05 (Amber Archive Jun 2010) (ambermd.org)<http://archive.ambermd.org/201006/0138.html>. On the other hand, I found it does for my alanine-in-12 A water box system when I rerun the trajectory.
Here is my sander input:
# md_rerun.in
&cntrl
imin=5,
ntx=5,
maxcyc=1,
irest=0,
temp0=300.0,
ioutfm=0,
ntwf=1,
ntwx=1,
cut=10.0,
ntb=1,
/
and in the output for cut=10:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -7.5647E+03 1.4040E+01 1.0199E+02 O 2168
BOND = 1.6571 ANGLE = 8.7221 DIHED = 12.0941
VDWAALS = 1079.3543 EEL = -8714.0624 HBOND = 0.0000
1-4 VDW = 3.0208 1-4 EEL = 44.5127 RESTRAINT = 0.0000
minimization completed, ENE= -.75647012E+04 RMS= 0.140397E+02
changing the cut=10 to cut=8 gives:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -7.4416E+03 1.3970E+01 9.7058E+01 O 2168
BOND = 1.6571 ANGLE = 8.7221 DIHED = 12.0941
VDWAALS = 1097.0112 EEL = -8608.5697 HBOND = 0.0000
1-4 VDW = 3.0208 1-4 EEL = 44.5127 RESTRAINT = 0.0000
minimization completed, ENE= -.74415517E+04 RMS= 0.139702E+02
As you can see, the EEL part changes from -8714.0624 to -8608.5697 kcal/mol, which is definitely not neglectable.
I wonder if any experts know what could be the probable reason.
Best regards,
Ge
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Received on Tue Aug 20 2024 - 07:00:02 PDT
