AMBER Archive (2003)

Subject: Re: problem about virtual box?

From: pengyo_at_rwja.umdnj.edu
Date: Thu May 01 2003 - 11:20:10 CDT

Dr. Simmerling:
  How to know if the molecule's center of mass is moving or not after
turing of centering? THe first and the last frames are looked at different
positions and totally seperated if saved and then loaded into moil-view
without centering. SO I think the center of mass may have moved during MD?
If I am wrong, please correct me.
 Thanks,
 Youyi Peng

Original Message:
-----------------
From: Carlos Simmerling carlos_at_csb.sunysb.edu
Date: Thu, 01 May 2003 11:46:05 -0400
To: pengyo_at_UMDNJ.EDU, amber_at_heimdal.compchem.ucsf.edu
Subject: Re: problem about virtual box?

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_at_UMDNJ.EDU>
To: <amber_at_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
>
>
>
>

--------------------------------------------------------------------
mail2web - Check your email from the web at
http://mail2web.com/ .