namd simulation​:protein,l​igand,lipi​d,water and ions

From: Marlet Martinez (marletm8_at_gmail.com)
Date: Tue Jun 19 2012 - 12:33:13 CDT

Dear all,

Thanks for your suggestions,

I already installed the 2.8 namd version but I cant run my simulation,
it stops again after message below comes (I already attached my .log
 file in the previous message). I am thinking maybe there is one problem
in my simulation because no matter what version I use (2.6 or 2.8) my
simulation stops automatically and coordinates are not even generated form
the 02.conf

-----------------------------

Info: CREATING 1716 COMPUTE OBJECTS

Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625

Info: NONBONDED TABLE SIZE: 769 POINTS

Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556

Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556

Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946

Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946

---------------

I would appreciate any suggestion,

Thanks in advance,

Mar,

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:09 CST