Hello,
I tried to minimize small molecule in vacuum condition with pmemd.cuda
[Amber 16, actualized].
Here is the content of the mdin file:
----------------
&cntrl
imin=1,maxcyc=5000,ncyc=4900,
ntb=0,
igb=6,cut=9999.0,
ntpr=100,
/
----------------
unfortunately the mdout file contained nonzero EGB component which is wrong
as with igb=6 this component should be zero.
-----------
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1699 2.2518E+01 9.0334E-05 1.8502E-04 H5 16
BOND = 0.2444 ANGLE = 0.1171 DIHED =
0.0070
VDWAALS = -0.7541 EEL = 0.2895 EGB =
19.7516
1-4 VDW = 3.9462 1-4 EEL = -1.0835 RESTRAINT =
0.0000
-----------
This pmemd.cuda problem appears just for minimization. For MD it is OK
(i.e. no EGB term is written in mdout)
I tested also sander and cpu version of pmemd (see below) and there is
everything OK so it is clearly
just problem of pmemd.cuda.
*** CPU pmemd output (minimization with above written settings)
-------------------------
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1181 2.6109E+00 8.2061E-05 1.8709E-04 H5 16
BOND = 0.1555 ANGLE = 0.1104 DIHED =
0.0065
VDWAALS = -0.7525 EEL = 0.3077 EGB =
0.0000
1-4 VDW = 3.8767 1-4 EEL = -1.0935 RESTRAINT =
0.0000
-------------------------
*** sander output (minimization with above written settings)
----------------
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1181 2.6109E+00 8.2061E-05 1.8709E-04 H5 16
BOND = 0.1555 ANGLE = 0.1104 DIHED =
0.0065
VDWAALS = -0.7525 EEL = 0.3077 EGB =
0.0000
1-4 VDW = 3.8767 1-4 EEL = -1.0935 RESTRAINT =
0.0000
----------------
Best wishes,
Marek
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Thu Feb 09 2017 - 07:30:03 PST
