AMBER Archive (2004)

Subject: Re: AMBER: sander, MD problems

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Nov 22 2004 - 06:53:29 CST

there are some postings in the archive about this, you might want to
read them. check:
http://amber.ch.ic.ac.uk/archive/200409/0008.html

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Kepa Koldo Burusco Goņi wrote:

>22-XI-2004
>
>Dear Amber users;
>
>I am trying to run some molecular dynamics of a box of solvent (299 molecules,
>100 Angstrom length, V = constant, gradually heating from 0K to 375K) in
>several machines with Amber7, but the calculations blow up unexpectedly when I
>try to run them on a LINUX PC server (SuSE 9.0).
>
>It is strange because the same files work correctly (and also slowly) in an
>older SGI Octane machine (much slower than the PC).
>
>I have checked the output files and the finale lines of "file.out" show this
>error message:
>********************************************************
>
>------------------------------------------------------------------------------
>--
> 4. RESULTS
>------------------------------------------------------------------------------
>--
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720
>| CHECK d/dx switch(x): max rel err = 0.7977E-11 at 2.712040
> ---------------------------------------------------
>| Local SIZE OF NONBOND LIST = 1013859
>| TOTAL SIZE OF NONBOND LIST = 1013859
> Exceeding lastrst
> lastrst = 2000000
> top_stk= 1050602
> isize = 1060904
> request= 2111506
> Increase lastrst in the &cntrl namelist
>******************************************************
>
>... It seems to be any kind of problem with "lastrst" option but I cannot find
>it in the manual...
>
>Do anyone have any idea? What should I do?
>I also send the "file.in" and "file.out" in case you need more information.
>
>Thank you very much in advance!!!
>
>Kepa K. Burusco Goņi
>e-mail; kepakoldo.burusco_at_campus.uab.es
>tfno: 0034 93 581 1266
>Universidad Autonoma de Barcelona
>Campus de Bellaterra
>BARCELONA
>Spain.
>
>
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