turn off centering in moil-view and
watch the trajectory again. go to
options/center/don't center
this will show you if the molecule's
center of mass is moving.
carlos
----- Original Message -----
From: "Youyi Peng" <pengyo.UMDNJ.EDU>
To: <amber.heimdal.compchem.ucsf.edu>
Sent: Thursday, May 01, 2003 11:49 AM
Subject: problem about virtual box?
> Dear AMBER fans:
> Last week I posted my problem about "the system has extended beyond
> the extent of the virtual box" and I got some helpful answers.
> Then I read the archive and found several similar posts to my problems.
> It looks two ways to solve the problem: one to check
> the trajectory and understand why it is changes so quickly, the other to
> modify "extraboxdim" in nonper.h file. I visualized the MD trajectory in
> moil-view and found the system shift a lot. My protein is a several
> transmembrane-helix protein. I did in vacuo MD on the protein-ligand
> complex. The last frame (at 236 ps) looks perpenticular to the first one
> (viewed in moil-view). But if I superimpose two conformations in
> InsightII, they look ok and the ligand still is in the binding pocket.
> It looks to me the whole complex in vacuo moves fast during MD
> simulation but the conformation of the complex doesn't change too much.
> Doesn't anybody has the similar experience? what should I do next? Maybe
> I need to modify the nonper.h file? By the way, which directory is
> nonper.h in? Any suggestion is more than welcome.
> The following are the error message for the output file and my input
> file for the MD simulation. I restarted the simulation and tried on both
> SGI and linux machines, but the problem still exists. The only
> difference is the job stopped at different time.
> Thanks a lot.
> Error message:
> Frac coord min, max: -2.1534132742728489E-06 0.7410054892789126
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
> Input MD file:
> dynamics w/o belly on protein, 9.0 cut, without constraints
> &cntrl
> nmropt = 0,
> ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,
>
> ntf = 1, ntb = 0,
> cut = 9.0, nsnb = 10, dielc=4.0
>
> ibelly = 0, ntr = 0,
>
> imin = 0,
> nstlim = 500000,
> nscm = 0,
> dt = 0.001,
>
> temp0 = 300.0, tempi = 300.0,
> heat = 0.0,
> ntt = 1,
> tautp = 2.0,
> vlimit = 20.0,
> ntc = 1, tol = 0.00001,
> &end
>
> &ewald
> eedmeth=5,
> &end
>
>
>
>
Received on Thu May 01 2003 - 16:53:01 PDT
