Dear Amber users,
I run a 250ps MD simulation on a Linux cluster (8 nodes) - it was performed
successfully with normal termination. However, the restart file (.xyz)
produced at the last step of simulation seems corrupted. When I was using
it to continue the simulation for another 250 ps this error message
appeared:
forrtl: severe (64): input conversion error, unit 10, file
/home/azmho/LIESUB1/sub1comp_mdI.xyz
Image PC Routine Line Source
sander 081F65A0 Unknown Unknown Unknown
Stack trace terminated abnormally.
p2_23575: p4_error: net_recv read: probable EOF on socket: 1
p3_24388: p4_error: net_recv read: probable EOF on socket: 1
p1_23989: p4_error: net_recv read: probable EOF on socket: 1
p4_24200: p4_error: net_recv read: probable EOF on socket: 1
p5_25190: p4_error: net_recv read: probable EOF on socket: 1
p7_25338: p4_error: net_recv read: probable EOF on socket: 1
p6_24035: p4_error: net_recv read: probable EOF on socket: 1
I also could not convert that particular restart file into .pdb file with
this error message:
[azmho.alpha LIESUB1]$ ambpdb -p sub1comp.prm <sub1comp_mdI.xyz>
sub1comp_mdI.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 12/14/04 Time = 20:43:08
forrtl: severe (64): input conversion error, unit 5, file stdin
Image PC Routine Line Source
ambpdb 080A8D90 Unknown Unknown Unknown
Stack trace terminated abnormally.
Do I have to re-run the simulation to produce uncorrupted restart file? It
already happened a few times and what I did is just re-run the simulation
and pray for an uncorrupted restart file...
Best regards and Happy New Year,
Bimo
---
Bimo Ario Tejo, Ph.D
Department of Biochemistry
Faculty of Biotechnology and Biomolecular Sciences
Universiti Putra Malaysia
43400 Serdang
Malaysia
e-mail: bimo.putra.upm.edu.my | http://www.biotech.upm.edu.my
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Received on Wed Dec 29 2004 - 05:53:01 PST
