> It works with nstlim = 100000 and position constraint 10.0.
You are saying it crashes on nstlim = 10000 but runs ok with
nstlim = 100000, for the same restraint energy of 10? This does
not make sense.
> But I found the carbon atoms are moving a lot
What kind of movement? (I see you are using constant volume, so
coordinate scaling would not be involved as it would be for
constant pressure.)
> (I didn't make bonds
> between the residues which have 2 carbon atoms because leap generates
> weird bonds longer than about 5~10 A)
That implies you bonded the wrong atoms. Bonding a whole sheet of carbons
seems like it would be difficult to get right, but possible. You need to
know how to name your residues/atoms for the bonds. Be sure to develop
the setup as a script for replicability.
> and I gave 10->5000 and NaN
> error was coming out again.
For the restraint weight? 5000 is very high, you could try 50.
Also, I will suggest gradual warming again.
> Do you think this structure setup is wrong?
I can't tell. E.g. you haven't described your residue unit.
Bill
> Thank you.
> Bongkeun Kim
> Quoting Bill Ross <ross.cgl.ucsf.EDU>:
> >> &cntrl
> >> imin = 0,
> >> irest = 0,
> >> ntx = 1,
> >> ntb = 1,
> >> cut = 10.0,
> >> ntr = 1,
> >> ntc = 2,
> >> ntf = 2,
> >> tempi = 0.0,
> >> temp0 = 300.0,
> >> ntt = 3,
> >> gamma_ln = 1.0,
> >> nstlim = 10000, dt = 0.002
> >> ntpr = 50, ntwx = 100, ntwr = 1000
> >> /
> >> Hold the graphite fixed
> >> 10.0
> >> RES 1 120
> >> END
> >> END
> >
> > You are warming the waters rapidly from 0 to 300K - you could
> > try warming slower.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> 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 Wed Oct 20 2010 - 11:30:06 PDT
