you haven't given enough information- how did you generate the initial
structure? how did you do the equilibration? are all of the force field
parameters standard, or did you create any new ones? what are you
restraining?
>
>
>
> Dear AMBER users,
>
> Recently, I tried to using solvatecap to simulate my system for faster
> speed. Unfortunately, sometime the ligands change drastically, even the
> ligand goes out the binding site in some simulation.
>
> I try to solve this problem using all kinds of ways:
> extending the cap radius;
> using smaller steps(0.001);
> adding some restraint;
> slowly increasing T;
> Unfortunately, the system is still not very stable as I expected. Here, I
> give the simulation file as follows and really hope anyone can give me some
> suggestions:
> #ntx=5,
> irest=1,
> imin=0,
> ntpr=1000,
> ntwx=1000,
> ntwr=5000,
> nstlim=250000,
> dt=0.001,
> ntt=3,
> gamma_ln = 1.0,
> temp0=300,
> tempi=300,
> tautp=1,
> igb=0,
> ntb=0,
>
> ntf=2,
> ntc=2,
> cut=15,
> ntr=1,
> fcap=2.5,
> ivcap=0,
> tol=0.000001,
> ntr=1, restraint_wt=5.0, restraintmask=':1-92, 95-144, 153-185, 200-243,
> 251-266, 273-288, 292-320, 324-326, 332-372, 375-377, 382-419',
> #I am really appreciated for your help!
>
> Rilei Yu
>
>
>
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>
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Received on Mon May 03 2010 - 17:00:04 PDT
