Re: colvar: atom group defn. fails

From: y_ja_at_163.com
Date: Fri Apr 16 2010 - 05:35:46 CDT

help; can you tell me how to cancel the e-mails like those that from namd-l.......... thank you. i'm look froward to your reply.

在2010-04-16 18:29:29，"Neelanjana Sengupta" <senguptan_at_gmail.com> 写é“：
Hi NAMD experts,

I am defining an rg colvar component as follows:

        gyration {
                # atom group definition:
                atoms {
                                atomsFile s1.pdb
                                atomsCol O
                                atomsColValue 2.0
                }
        }

However, NAMD fails to recognize this atom group definition, and complains:

colvars: Initializing atom group "atoms".
colvars: Error: no atoms defined for atom group "atoms".

I could not figure out the problem here. I have used a similar module for a reference structure in RMSD (refPositionsFile, refPositionsCol, refPositionsColValue), and that had worked...

Some pointers would be very helpful.

Thanks,
Neelanjana

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