[gmx-users] 2 Questions

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 11 00:04:54 CET 2011

simon sham wrote:
> Hi,
> I) I have been trying to figure out where is the source of the following 
> warning message coming from:
> WARNING: masses and atomic (Van der Waals) radii will be determined
>          based on residue and atom names. These numbers can deviate
>          from the correct mass and radius of the atom type.

It would be useful to know what program is issuing this statement, what your 
command was, what you're doing, etc.  Presumably, whatever program it is needs 
van der Waals radii and is going to make a guess as to what they should be based 
on atom names rather than types.  Using a run input file usually alleviates this 

> 2). I used ngmx to inspect the trajectory of a 20ns MD run, and I 
> noticed that the protein is moving around quite a bit in different 
> directions. Is it normal?

All molecules diffuse.  Otherwise, see FAQ #11, which is a question that gets 
asked weekly, if not more frequently.



> Thanks for your insight.
> Simon


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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