Hi,
I am having some problems in running sander on an extremely simple system:
Dihydrogen-phosphate anion. (all atoms model)
I have used this input file for a short minimization:
&cntrl
imin=1, maxcyc=5000, ncyc=50, drms=0.1, scee=1.2,
ntb=0,
&end
And then a MD simulation like this:
&cntrl
irest=0, ntx=1, ntb=0, ntnb=1, nsnb=999999,
ntwx=500, ntwe=500,
ntf=3, scee=1.2, cut=1000,
init=3, nrun=1000, nstlim=500, dt=0.002,
temp0=300.0, ntt=1,
ntc=3, ntcm=1, nscm=500,
iftres=0,
&end
The prep file has been thoroughly checked and both xleap and the old
LINK/EDIT/PARM protocol have been followed in building the system.
The behaviour in MD is a bit strange, with huge 1-4 EEL terms, and a final
SHAKE failure, which I attribute to a great motion on the molecule. When I
remove SHAKe from the input, temperature rises until clearly artifactual
values.
The same simulation on Phospate anion (charge = -3 ) has given no prblems at
all. What happens when introducing the 1-4 terms?
Any suggestion will be well recieved. Thanks a lot in advance,
Blas
For those who want, here is the prep file:
0 0 0
H2PO4
JIP.dat
JIP INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000
2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000
3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000
4 HO1 EH M 3 2 1 0.82 135.03 222.18 0.4310
5 OH1 EO M 4 3 2 1.02 50.84 231.69 -0.7460
6 P MP M 5 4 3 1.65 109.46 9.68 1.2460
7 O1P MO E 6 5 4 1.66 109.75 212.00 -0.8080
8 O2P MO E 6 5 4 1.65 109.39 350.00 -0.8080
9 OH2 EO M 6 5 4 1.66 109.34 102.00 -0.7460
10 HO2 EH M 9 6 5 1.02 109.05 102.00 0.4310
DONE
STOP
Received on Fri Jan 26 2001 - 10:18:20 PST
