[gmx-users] Problem in generation of tpr file

Justin Lemkul jalemkul at vt.edu
Tue Jun 12 16:27:19 CEST 2018

On 6/11/18 2:42 PM, Alex wrote:
> To be clear, I did suggest ignoring it _only_ if the warning is: a) 
> understood, b) of known origin, and c) harmless. I am not sure what's 
> your one case is when ignoring warnings is appropriate, but I 
> routinely use '-maxwarn 10,' because I have a bunch of bonded 
> parameters that override default stuff in ffbonded for DNA (I think 
> this customization came from Tsjerk Wassenaar when we collaborated). 
> The warnings appear even when no DNA is present in the system, but in 
> either case I know exactly what I am doing.
> In no way should new users interpret my suggestion as "it is okay to 
> ignore grompp warnings." It is NOT okay to ignore them.

Right, and I only pointed it out because the OP seemed confused about 
what's going on, so I felt it important to reinforce the fact that new 
users should never use this option.

The one case I remember requiring -maxwarn was with MARTINI, which set 
up dummy atom names in its coordinate files, only to be corrected later 
in grompp so that the topology atom names were used. This appears to no 
longer be the case, so I can now think of precisely ZERO times that 
-maxwarn should be employed in common usage.

Your broken, conflicting force fields would be an intermediate-level 
exception :) The problem I've seen is when people see existing 
scripts/workflows with -maxwarn 10 (living dangerously!) then it gets 
propagated without thought. Hopefully all of your scripts and protocols 
come with the comment of "DON'T DO THIS GENERALLY" :)


> Alex
> On 6/11/2018 6:04 AM, Justin Lemkul wrote:
>> Please don't respond to the entire digest, and if you're actively 
>> asking questions, I suggest changing your list subscription to 
>> receive individual emails.
>> On 6/11/18 6:51 AM, Rahma Dahmani wrote:
>>> sorry, i am new Gromacs user, where i can find the warning text ?
>> grompp prints very clear and obvious WARNINGs to the terminal. Read 
>> what it says.
>> I disagree with Alex's suggestion that using -maxwarn might be 
>> appropriate. There's basically only one case I can think of when this 
>> is ever reasonable, yet I see people get in trouble all the time when 
>> they start making a habit of using -maxwarn. grompp is trying to tell 
>> you that what you are doing is physically unreasonable. Don't ignore it.
>> -Justin


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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