AMBER Archive (2004)

Subject: AMBER: sander, MD problems

From: Kepa Koldo Burusco Goņi (
Date: Mon Nov 22 2004 - 06:00:37 CST


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 "" and "file.out" in case you need more information.

Thank you very much in advance!!!

Kepa K. Burusco Goņi e-mail; tfno: 0034 93 581 1266 Universidad Autonoma de Barcelona Campus de Bellaterra BARCELONA Spain.

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