[gmx-users] Help for gmx enemat

[Peter Stern]

I believe that you need to define which nucleotides are in each group DNA1 and DNA2 using make_ndx, since those are not "default" groups.  I think that you can do this and then do an Metin -rerun just to define the new groups.

Peter

Sent from my iPad

> On 13 בינו׳ 2016, at 20:53, valerio di giulio <digiuliovalerio at gmail.com> wrote:
> 
> Hi,
> 
> I have a problem with the use of "gmx enemat". I'm trying to calculate
> the contribution of SH-LJ to the potential that exists between two DNA
> strands with GROMACS 5.1.1. I've already got a Potential of Mean Force
> doing an umbrella sampling.
> For this reason I have already many files .edr each one linked to a window,
> from
> which I would like to extract the SH-LJ contribution but every time I use
> "enemat" this is the output:
> 
> ......................
> 
> GROMACS:      gmx enemat, VERSION 5.1.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>  gmx enemat umbrella1e.edr -ljsr
> 
> Opened ener.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file
> WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
> WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
> WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file
> WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file
> 
> Will select half-matrix of energies with 0 elements
> Last energy frame read 500 time  500.000
> Will build energy half-matrix of 2 groups, 0 elements, over 501 frames
> Segmentation fault (core dumped)
> 
> ...........................
> 
> Although I have written to the .mdp file:
> 
> energygrps = DNA1 DNA2
> 
> Thank you in advance,
> 
> Valerio Di Giulio
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