[gmx-users] Regarding the measuring potential Ene of peptide ..

rama david ramadavidgroup at gmail.com
Thu Dec 27 14:59:47 CET 2012

Hi gromacs Friends,

I  simulated the system containing two peptide which are kept at 2 nm
apart from each other.
When I simulated them, they come close to each other and start interact
with  each other.

I want to check the
 1. change in pot energy of two peptide ,
 2. hydrophobic interaction energy
 3. Change in entropy of sol and peptide

I make new mdp file containing  the energygrps protein1 and protein2
I rerun the mdrun
Now When I gave the command g_enemat it replied like

Opened md-rerun.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):protein1-protein1 (0,0)in
energy file
WARNING! could not find group (null):protein1-protein2 (0,1)in energy file
group 1WARNING! could not find group (null):protein2-protein2 (1,1)in
energy file

Will select half-matrix of energies with 6 elements
Last energy frame read 100000 time 100000.000
Will build energy half-matrix of 2 groups, 6 elements, over 100001 frames
Segmentation fault (core dumped)

I face the same problem in another system also...

please tell me the command to check entropy and hydrophobic interaction..

I will be greatly thank-full for your  help.

With best wishes and regards
Rama david

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