AMBER: Restrained minimization problem

From: <opitz.che.udel.edu>
Date: Mon, 29 Nov 2004 17:11:56 -0500
('binary' encoding is not supported, stored as-is) Dear Amber Community,

I am starting an explicit solvent simulation in Amber7. As suggested in
the amber manuals, I at first run a minimization with the solute
restrained. The solute is quite large with 4548 atoms.
When I start the simulation the job quits very quickly with the following
message:
5. REFERENCE ATOM COORDINATES

                                                                                  
    ----- READING GROUP 1; TITLE:
 Group input for restrained atoms

     GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
 GRP 1 RES 1 TO 249
      Number of atoms in this group = 4548
    ----- END OF GROUP READ -----
 Exceeding lastist in get_istack
   lastist = 2000000
   top_stk= 1786044
   isize = 232008
   request= 2018052
  Increase lastist in the &cntrl namelist

The input file is as follows:
&cntrl
 imin = 1,
 maxcyc = 1500,
 ncyc = 500,
 ntb = 1,
 igb = 0,
 cut = 12,
 ntr = 1,
&end
Group input for restrained atoms
 500.0
RES 1 249
END
END


Does this mean that the entire system is too large or is it just
something concerning the restraining command? How can I resolve this
problem to move on?

Best Regards,

Armin


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Nov 29 2004 - 22:53:00 PST
Custom Search