Re: restart problem

From: Marcos Sotomayor (
Date: Fri Dec 02 2005 - 00:10:18 CST

Dear Xin Liu,

The *.coor and *.vel files are binary files, therefore you need
to replace "coordinates" by "bincoordinates" and "velocities" by
"binvelocities". You may want to keep "coordinates original-file.pdb".


  On Fri, 2 Dec 2005, liu xin wrote:

> Dear namd-users:
> My simulation stopped at step 231000, I wanted to restart it at thisstep, I added the two lines below to the .conf file:
> velocities ../common/zgxjlx_wb_eq.restart.velextendedSystem ../common/zgxjlx_wb_eq.restart.xsc
> and changed the line:
> coordinates ../common/ubq_wb_eq.coor
> to:
> coordinates ../common/ubq_wb_eq.restart.coor
> after that I commented out the line specified the tempreture, set the"firsttimestep" to 231000. Then I did the namd run and got thefollowing error:
> ------------- Processor 0 Exiting: Called CmiAbort ------------Reason: FATAL ERROR: Line too long in pdbfile../common/zgxjlx_wb_eq.restart.coor:?üBøt9A@:²D▒±à@9?ñ¸ ×@¶Ü XÉ@:@%åîd¦@9¡~iQ?þñD2ÐÉû@9<q£n¿@8´ø#G*@l§tÎ@8Áñ|Þ1?@9d0Uõ¥@BM&@9Uo³8_at_7ᥦ(r)A@ òI¼mï@:GÇÆ~@8rBC7@ïÕ6
> Charm++ fatal error:FATAL ERROR: Line too long in pdbfile ../common/zgxjlx_wb_eq.restart.coor:?üBøt9A@:²D▒±à@9?ñ¸ ×@¶Ü XÉ@:@%åîd¦@9¡~iQ?þñD2ÐÉû@9<q£n¿@8´ø#G*@l§tÎ@8Áñ|Þ1?@9d0Uõ¥@BM&@9Uo³8_at_7ᥦ(r)A@ òI¼mï@:GÇÆ~@8rBC7@ïÕ6
> I remebered that someone've met this "line too long" error before, inthat case he used the "bincoordinates" option to solve the problem,since I haven't used the "binaryoutput" option, I think this methodcan't help my problem. In my case, I think my .restart.coor file arepdb file, but when I checked my .restart.coor and file, I found it full of symbols, numbers and letters like the error message showed,this is not in the same format of pdb files I saw before, so I doubtif the problem is here? My system is SUSE 9.0 and I used the NAMD 2.5to do the simulation.
> Any suggestions will be highly appreciated!
> Xin Liu

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