[gmx-users] Fwd: Regarding the measuring potential Ene of peptide ..
ramadavidgroup at gmail.com
Fri Dec 28 14:23:54 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
To check the pot energy of two 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
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
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
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