Subject: help:NAMD2

From: [email-masked]
Date: Thu, 4 Mar 1999 11:33:08 +0900

Dear CCLers,

   Could someone help me to solve a problem with a MD simulation using
namd2.

I downloaded namd2.0b3(binary) from the namd homepage and installed
on my SGI machine(octance R10000 250MHz, 2cpu, IRIX6.4).
When I ran a MD simulation with a periodic boundary condition, the job
stopped
with the following messages.

 .....
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 1012 ATOMS
Info: 11 BONDS
Info: 18 ANGLES
Info: 16 DIHEDRALS
Info: 2 IMPROPERS
Info: 0 EXCLUSIONS
Info: 3033 DEGREES OF FREEDOM
Info: 1005 HYDROGEN GROUPS
Info: *****************************
Info: Entering startup phase 0
Info: Entering startup phase 1
Info: Entering startup phase 2
Info: Entering startup phase 3
Info: PATCH GRID IS 69 (PERIODIC) BY 69 (PERIODIC) BY 69 (PERIODIC)
Info: REMOVING COM VELOCITY ( -0.1068, 0.0186864, -0.00757281)
Info: 1012 atoms assigned to node 0
ID's not allocated in ComputeMap::storeCompute().
############### END of the log-file ###############

The sample job attached to the program(MD of alanine oligopeptide) runs
without any problem.

Any comments or suggestions are appreciated.

Thanks in advance,

                   Takanori Kanazawa

***************************************************************
                   Takanori Kanazawa
                   E-mail : [email-masked]

                   Drug Discovery Group / CAMM
                   Takarazuka Research Institute
                   Novartis Pharma K.K.
                   10-66 Miyuki-cho, Takarazuka, Hyogo 665
                   JAPAN
***************************************************************