Hi,
I am trying to equilibrate my protein system using SANDER in AMBER6.
My system has more than 40,000 atoms. At first I am minimizing my system
and it is working well. However, when I start MD with the minimized
structure (with RMS 1.1925E-01 and GMAX 4.7164E+00 - which seems to be not
to bad for my huge system) , I can not use default time step of 0.001
- it works for 0.0005. My system has waters made by 'solvatewatbox 216 10'
command in Leap.
I tried to do a vacuum simulation without the waters and it works
fine. Thus it seems at least the structure of the protein is OK. Probably
the problem is with the waters. I am using PME and a cutoff of 9.0. I
tried to increase the cutoff - but then it crashes too with a message
- system is too inhomogenous.
With cutoff=9.0 and PME the error message is ( it is running for 20
steps and then crashes);
forrtl: error (75): floating point exception
forrtl: error (75): floating point exception
Below is my input file for MD. I would appreciate very much if anyone can
help me with my problem. Thanks.
Pradipta
# water MD 35ps
&cntrl
imin=0,
ntx=1, irest=0, ntrx=1,
ntxo=1, ntpr=1, ntwr=1000, ntwx=500, ntwe=500,
ntf=2, ntb=2, dielc=1, scnb=2, scee=1.2,
nstlim=17500, ntcm=0, nscm=0, t=0.0, dt=0.001,
temp0=50, tempi=10.0, ntt=1, tautp=2.0,
ntp=1, taup=0.2, npscal=0,
ntc=2, tol=0.0002,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
&end Group input for restrained atoms
25.0 RES 1 272 END END
Received on Thu Jun 14 2001 - 10:16:59 PDT
