From: francesco oteri (francesco.oteri_at_gmail.com)
Date: Mon Apr 26 2010 - 05:12:04 CDT
Hi,
i've experienced the same problem with a globular protein in water.
In particular i did some observation:
1) NAMD hangs between file writing and energy evaluation ( or output ).
For example:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 243250
WRITING COORDINATES TO DCD FILE AT STEP 243250
WRITING COORDINATES TO RESTART FILE AT STEP 243250
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 243250
FINISHED WRITING RESTART VELOCITIES
ENERGY: 243500 493.7421 1443.4799 515.5054
102.9102 -388484.8485 36829.5168 0.0000
0.0000 65081.7699 -284017.9242 301.3271 -349099.6941
-283859.6549 300.0469 58.1440 117.6399
1066890.2675 2.2563 2.4422
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 243500
WRITING COORDINATES TO DCD FILE AT STEP 243500
WRITING COORDINATES TO RESTART FILE AT STEP 243500
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 243500
FINISHED WRITING RESTART VELOCITIES
As you can see, in the last writing operation there is no "ENERGY:" line,
while it is present in the previous.
2) When i do "strace -p pid" i obtain that the system is trapped into an
infinite series of "poll" system call.
Inspecting the code, i found that this system call is present in some
charm-6.1.3 source file, but i'm not still able to detect where the
charm-namd connection appears.
3) If I compile the package, hanging is more frequent.
Have you observed the same behaviour?
I will introduce some debug printf to detect the error source.
If anyone has some suggestions?
2010/4/26 Ning Zhang <zhangning19850204_at_hotmail.com>
> Hi everyone:
> I am doing my job following the membrane-tutorial with another
> membrane-protein.
> When melting lipid tails, at the beginning the simulation runs well.
> But at some step, the simulation seems to be in a endless loop, and the
> .log file is not written.
> Has anyone experience it ?
> Auy help will be appreciated.
>
> ---------------------------------------------------------------
> *Ning Zhang, Ph.D. Student*
> *School of Energy and Power Engineering*
> *Dalian University of Technology*
> *Dalian 116021, China*
> ---------------------------------------------------------------
> zhangning19850204_at_hotmail.com<%3C%21--AID_FROMADDRESS_BEGIN--%3Ezhangning19850204_at_hotmail.com%3C%21--AID_FROMADDRESS_END--%3E>
> 2010-04-26
>
-- Cordiali saluti, Dr.Oteri Francesco
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