Dear gmx users,
I downloaded POPE.itp and lipid.itp files from Dr.Tieleman
website http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
and POPG.itp file from Dr.Mikko Karttunen wesite
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml.
I built a POPE:POPG bilayer in 3:1 ratio. When I am minimizing the bilayer,
bonds in head groups are breaking in POPE and POPG lipid molecules.
Here is my min.mdp input file
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 2000
;
; Energy minimizing stuff
;
emtol = 100
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
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while creating *.tpr file using the above file for minimization, I am getting
fallowing message.............
calling /lib/cpp...
In file included from pg-pe.top:5:
dpopg.itp:10:8: warning: multi-line string literals are deprecated
processing topology...
Generated 344865 of the 344865 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 344775 of the 344865 1-4 parameter combinations
Excluding 3 bonded neighbours for POP 48
Excluding 3 bonded neighbours for DPO 16
Excluding 2 bonded neighbours for SOL 2481
NOTE:
System has non-zero total charge: -1.599999e+01
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# BONDS: 8242
# ANGLES: 6257
# PDIHS: 1712
# RBDIHS: 1472
# IDIHS: 272
# LJ14: 1840
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 10787 elements
Making dummy/rest group for Acceleration containing 10787 elements
Making dummy/rest group for Freeze containing 10787 elements
Making dummy/rest group for Energy Mon. containing 10787 elements
Making dummy/rest group for VCM containing 10787 elements
Number of degrees of freedom in T-Coupling group rest is 32358.00
Making dummy/rest group for User1 containing 10787 elements
Making dummy/rest group for User2 containing 10787 elements
Making dummy/rest group for XTC containing 10787 elements
Making dummy/rest group for Or. Res. Fit containing 10787 elements
Making dummy/rest group for QMMM containing 10787 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...
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My question,
Why bonds are breaking in POPG and POPE lipid molecules.
Any suggestion is appreciated.
Thank you in advance.
with regards,
Nagaraju Mulpuri.
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