[gmx-users] gmx rmsdist: rmsmax vs. rmscmax

[Alan Manning]

Hi, thanks for the reply.

I now have another question regarding the the rmsdist tool: I'm confused 
why my rmsmax value seems so small. Right now I am simulating a box of 
water only. I'd like to get a matrix of all the atom-atom distances for 
a single frame in my simulation, so use the following command:

gmx rmsdist -f nvt.trr -s nvt.tpr -mean -nosumh -b 100 -e 100

However, this gives an rmsmax = 0.000345129, which is smaller than a 
water molecule, and I"m not sure why.

I'm also curious why I need to supply a topology file if all I want to 
calculate is the interactomic distances. I'm likely misunderstanding 
this tool... Thanks in advance for the help.

Regards,
Alan Manning



On 03/16/15 04:24, Justin Lemkul wrote:
>
>
> On 3/15/15 6:36 PM, Alan Manning wrote:
>> Hi
>>
>> What is the difference between the "rmsmax" and "rmscmax" values
>> written to the
>> screen when running "gmx rmsdist"? Thanks.
>>
>
> rmscmax is scaled by dividing by the mean ("sc" for "scaled,"
> presumably).  See calc_rmsd() in gmx_rmsdist.c
>
> -Justin
>