On 7/6/13 8:21 AM, rama david wrote:
Hi Friends,
I am working on peptide self assembly.
I simulated two peptide which are random coil and apart from each other.
As the time process they start to interact and form antiparallel beta sheet
structure.
My plan is to find the energy difference in random coil to beta
shhet structure.
I added protein1 protein2 group in mdp file I run g_energy coomand
Output:
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 G96Angle 2 Proper-Dih. 3 Improper-Dih. 4
LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8
Disper.-corr.
9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12
Kinetic-En.
13 Total-Energy 14 Temperature 15 Pres.-DC 16
Pressure
17 Constr.-rmsd 18 Box-X 19 Box-Y 20
Box-Z
21 Volume 22 Density 23 pV 24
Enthalpy
25 Vir-XX 26 Vir-XY 27 Vir-XZ 28
Vir-YX
29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32
Vir-ZY
33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36
Pres-XZ
37 Pres-YX 38 Pres-YY 39 Pres-YZ 40
Pres-ZX
41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44
Box-Vel-XX
45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X 48
Mu-Y
49 Mu-Z 50
Coul-SR:protein1-protein1
51 LJ-SR:protein1-protein1 52
LJ-LR:protein1-protein1
53 Coul-14:protein1-protein1 54
LJ-14:protein1-protein1
55 Coul-SR:protein1-protein2 56
LJ-SR:protein1-protein2
57 LJ-LR:protein1-protein2 58
Coul-14:protein1-protein2
59 LJ-14:protein1-protein2 60
Coul-SR:protein1-rest
61 LJ-SR:protein1-rest 62
LJ-LR:protein1-rest
63 Coul-14:protein1-rest 64
LJ-14:protein1-rest
65 Coul-SR:protein2-protein2 66
LJ-SR:protein2-protein2
67 LJ-LR:protein2-protein2 68
Coul-14:protein2-protein2
69 LJ-14:protein2-protein2 70
Coul-SR:protein2-rest
71 LJ-SR:protein2-rest 72
LJ-LR:protein2-rest
73 Coul-14:protein2-rest 74
LJ-14:protein2-rest
75 Coul-SR:rest-rest 76
LJ-SR:rest-rest
77 LJ-LR:rest-rest 78
Coul-14:rest-rest
79 LJ-14:rest-rest 80
T-Protein
81 T-non-Protein 82
Lamb-Protein
83 Lamb-non-Protein
.But when I gave the command :
g_enemat_mpi -f ../energy.edr -groups groups.dat -etot ener.xvg
I ended with following Missery :
Opened ../energy.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 200000 time 200000.000
Will build energy half-matrix of 2 groups, 6 elements, over 200001 frames
Segmentation fault (core dumped)
This problem has been posted several times before and looks buggy to me. Please
open a redmine issue and provide a sample input file that reproduces the problem.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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