AMBER Archive (2008)

Subject: AMBER: minimization stops or does not write anything

From: rebeca_at_mmb.pcb.ub.es
Date: Thu Aug 14 2008 - 04:01:17 CDT

Hello,
I am trying to minimize a membrane+protein system (solvated and with ions) that
has more than 700,000 atoms.
In a local cluster, the calculation begins, but then it is not kill, but stops
writting in this point:

File Assignments:
| MDIN: min_ntr_50_all.in
| MDOUT: min_ntr_50_all.o
|INPCRD: equilibrado_amber.crd
| PARM: equilibrado_amber.top
|RESTRT: min_ntr_50_all.r
| REFC: equilibrado_amber.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

 #minimisation of waterbox with restraints on all protein atoms
 &cntrl
  imin=1, maxcyc=5000, ncyc=5000, drms=0.01, ntb=1, ntr=1,
 /
Group input for restrained atoms
 50.0
RES 1 2565
END
END

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info not found in inpcrd
|Largest sphere to fit in unit cell has radius = -0.021

When I tried it in another cluster (Marenostrum), it does not even begin to
write anything. The calculation is not killed, it creates an empty output file,
but does not write anything on it.

Does anybody know what could be happening? Is there any atom limit calculation
to calculate in Amber?

Thank you very much for your help.

PD: I am using Amber9

Rebeca García Fandiño
Parc Cientific de Barcelona

The calculation does not write anything

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