On 10/18/2006 8:10 AM, Aline Rossi wrote:
Hi list,
Im dealing with a problem when trying to monitoring energygrps. When I
run the grompp i receive this output:
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for Protein_C 1
Excluding 2 bonded neighbours for SOL 30314
Excluding 1 bonded neighbours for NA+ 2
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 312 K
renumbering atomtypes...
converting bonded parameters...
# G96BONDS: 6825
# G96ANGLES: 9964
# PDIHS: 3583
# IDIHS: 3430
# LJ14: 10944
# SETTLE: 30314
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 90944 elements
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131
Fatal error:
Not enough ref_t and tau_t values!
my index file is:
0 System : 96772 atoms
1 Protein : 6694 atoms
2 Protein-H : 5213 atoms
3 C-alpha : 666 atoms
4 Backbone : 1998 atoms
5 MainChain : 2667 atoms
6 MainChain+Cb : 3268 atoms
7 MainChain+H : 3306 atoms
8 SideChain : 3388 atoms
9 SideChain-H : 2546 atoms
10 Prot-Masses : 6694 atoms
11 Non-Protein : 90078 atoms
12 Mg : 7 atoms
13 SOL : 90069 atoms
14 NA+ : 2 atoms
15 Other : 90078 atoms
16 alpha&beta : 6648 atoms
17 his159 : 12 atoms
18 arg157 : 17 atoms
19 ecdw : 51 atoms
20 glu1 : 12 atoms
21 cys2 : 8 atoms
22 asp3 : 9 atoms
23 trp4 : 22 atoms
24 tyr458 : 18 atoms
25 ala585 : 6 atoms
26 prot+pep : 6703 atoms
27 prot+pep+mg : 6706 atoms
28 alpha : 4453 atoms
29 beta : 2202 atoms
30 pep : 51 atoms
title = PEP MD
cpp = /lib/cpp
constraints = none
integrator = md
dt = 0.0015 ; ps !
nsteps = 10000000 ; total 500 ps.
nstcomm = 3000
nstxout = 3000
nstvout = 5000
nstfout = 3000
nstlog = 1500
nstenergy = 3000
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
unconstrained-start = yes
; Berendsen temperature coupling is off in two groups
Tcoupl = berendsen
tc-grps = alpha beta pep
tau_t = 0.1 0.1 0.1
ref_t = 312 312 312
; Energy monitoring
energygrps = alpha beta pep
beside the proteins, solvent also needs t-coupl.
Try this
tc-grps = alpha beta pep rest
tau_t = 0.1 0.1 0.1 0.1
ref_t = 312 312 312 312
; Energy monitoring
energygrps = alpha beta pep rest
; Isotropic pressure coupling is on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 312 K.
gen_vel = yes
gen_temp = 312.0
gen_seed = 173529
What should be wrong with my imputs??
Thanks for help
and my .mdp file is:
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