AMBER Archive (2009)

Subject: [AMBER] Parallel sander & polarisability

From: Thomas Taylor (thomas.taylor_at_univie.ac.at)
Date: Thu Oct 29 2009 - 11:19:14 CDT

Dear Amber Users,

PMEMD clearly does not support polarisation (stated on p.200 in the Amber 10
manual) - unless using the amoeba forcefield, which I do not. Sander on the
other hand does, but the parallel version seems not to work so well, it
crashes with an internal fortran error, having trouble converting something
from the prmtop file.

My Amber (and all mentioned versions of sander and chamber) is actually some
approx. 1 month old checkout of the amber11 cvs. The prmtop files are generated
via chamber (which I costumised to translate polarisabilities).

Here is a short table of what works and what does not:

sander prmtop polarisability script status
serial no such section ipol=0 WORKS
serial specified, all set to 0 ipol=0 WORKS
serial specified, values > 0 ipol=1 WORKS
parallel specified, all set to 0 ipol=0 WORKS
parallel specified, values > 0 ipol=1 CRASHES

Let me again stress the fact that all versions of sander have been compiled
from the same sources. Also I verified that the prmtop files differ only in the
POLARIZABILITY section. The input scripts in all cases are identical, but for
ipol, which is either 0 or 1.

Please let me know if polarisability should work in parallel sander and if so
what I can do to fix this problem or how I can help to identify the root of
this problem.

Thank you!
Thomas Taylor

PS: The rather not so helpful error traceback:
forrtl: severe (64): input conversion error, unit 8, file
/home/lv70041/ttaylor/rtil/amber/emim_trif_200/duijnen_8/./emim_trif_200.prmtop
Image PC Routine Line Source
sander.MPI 0000000000ACCF5D Unknown Unknown Unknown
sander.MPI 0000000000ACBA65 Unknown Unknown Unknown
sander.MPI 0000000000A688C9 Unknown Unknown Unknown
sander.MPI 0000000000A052FD Unknown Unknown Unknown
sander.MPI 0000000000A04B4A Unknown Unknown Unknown
sander.MPI 0000000000A2F7FB Unknown Unknown Unknown
sander.MPI 00000000004F29A3 Unknown Unknown Unknown
sander.MPI 00000000004D755D Unknown Unknown Unknown
sander.MPI 00000000004D71C9 Unknown Unknown Unknown
sander.MPI 0000000000404A4C Unknown Unknown Unknown
libc.so.6 00002B691ECC8974 Unknown Unknown Unknown
sander.MPI 0000000000404959 Unknown Unknown Unknown 

-- 
Just because everything is different doesn't mean anything has changed.
		-- Irene Peter

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