AMBER Archive (2005)

Subject: RE: AMBER: Error in "restrt" output file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Sep 14 2005 - 16:46:40 CDT

Dear Alexander,
 
The stars are printed when the value is too large to fit in the space
allocated, in this case F12.7 meaning a maximum value of 9999.9999999 and a
minimum value of -999.9999999. Some of your coordinates have exceeded this.
This can happen for several reasons. Potentially you did remove centre of
mass motion (nscm=0) and so your system has diffused over time or
alternatively you are running a periodic simulation and some of your waters
have diffused a long way from the original box. You have two options, the
first is to take the last restart file that was okay and use ptraj to image
the coordinates back into the central box. You can then use this restart
file to continue your MD run.
 
Alternatively you can take the last restart file that works and restart the
simulation but select to write binary restart files instead of ascii. These
will not be human readable but will not suffer from the range limitations of
ascii restart files. (NTXO=0).
 
All the best
Ross
 

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Alexander Rubinstein
Sent: Wednesday, September 14, 2005 14:31
To: amber_at_scripps.edu
Subject: AMBER: Error in "restrt" output file

Dear AMBER users,

I would like to carry out a long time high temperature MD simulation for 30-
residue peptide in explicit water by ABMER 7. I am performing all
calculations on the Beowulf cluster containing 32x nodes Atipa Dual-Xeon
(32x Xeon 3.06 GHz and 32x Xeon 2.4 GHz) running RedHat Linux 7.3. I have
done it for time simulations over 10 ns by multiple runs 200-400 ps, but
after some runs errors become in the output coordinate
 "restrt" file - the final set of coordinates from the MD run.

I would very appreciate if some one helps me to find out this problem.
Please find enclosed below the relevant files:

sander_53_PP_p3.o1738:
Date: Wed Aug 10 11:28:47 CDT 2005
The master node of this job is node027
The working directory is /home/......../MD_PPII_T500
The node file is /usr/spool/PBS/aux/1738.head
This job runs on the following nodes:
node027 node027 node026 node026 node025 node025 node024 node024
This job has allocated 8 cpus
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

PGFIO-F-231/formatted read/unit=9/error on data conversion.
 File name = md_52_Ab40_WN.xyz formatted, sequential access record = 3254
 In source file _ew_setup_.f, at line number 3260
p7_13395: p4_error: net_recv read: probable EOF on socket: 1
p6_13386: p4_error: net_recv read: probable EOF on socket: 1
p5_13395: p4_error: net_recv read: probable EOF on socket: 1
p3_13395: p4_error: net_recv read: probable EOF on socket: 1
p4_13386: p4_error: net_recv read: probable EOF on socket: 1
p2_13386: p4_error: net_recv read: probable EOF on socket: 1
bm_list_14395: (0.195413) wakeup_slave: unable to interrupt slave 0 pid
14394
p1_14398: p4_error: net_recv read: probable EOF on socket: 1
bm_list_14395: (0.195510) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195574) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195610) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195648) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195690) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195756) wakeup_slave: unable to interrupt slave 0 pid
14394

md_52_Ab40_WN.xyz ("restrt" file):
  
line 1 > 17267 0.1160200E+05
           -46.8339026 188.5295923 38.0942556 -45.8985398 188.1987971
37.9051236
           .................................................
           .................................................
line 3254> 310.0074935 299.7106465 -96.1944303 116.7414444
-30.3483541************
           116.4267112 -31.2457463************ 116.9960680
-30.0752141************
           -97.6000294-125.1316991 265.1031660 -97.6053942-124.2881423
264.6508223
           .................................................
           .................................................
           -0.3018643 -0.0648276 0.3413060 -0.6228245 0.8959412
0.4736578

Alexander Rubinshtein, Ph.D.
UNMC Eppley Cancer Center
Molecular Modeling Core Facility
_________________________________
University of Nebraska Medical Center
986805 Nebraska Medical Center
Omaha, Nebraska 68198-6805
USA
Office: (402) 559-7809
Fax: (402) 559-4651
E-mail: arubin_at_unmc.edu
WWW: http://www.unmc.edu/Eppley

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