[gmx-users] oplsaa and lincs error

[MURAT CETINKAYA]

Hi gmx users,

I am trying to perform Free Energy calculations on a non-standard residue using
oplsaa force field. Two problems arise:

1) When I try to minimize in vacuo, atoms split apart and molecule is destroyed.
This is independent of the algorithm. I tried with and witohut constraints on
the system. This is the input file for in vacuo:

title                    = EM  in vacuo
cpp                      = /lib/cpp
include                  = -I/./
integrator               = steep
nbfgscorr                = 50
nstcgteep                = 1
nsteps                   = 5000
emtol                    = 1
niter                    = 20

nstxout                  = 10
nstvout                  = 0
nstfout                  = 0
nstlog                   = 10
nstenergy                = 10
nstxtcout                = 0
xtc-precision            = 100
xtc_grps                 = Protein
energygrps               = Protein 

nstlist                  = 1
ns_type                  = grid
;pbc                      = xyz
rlist                    = 1.0
coulombtype              = PME
rcoulomb                 = 1.0
epsilon_r                = 1.0
vdw-type                 = Cut-off
rvdw                     = 1.0
constraints              = all-bonds
; EWALD/PME/PPPM parameters 
pme_order                = 12
ewald_rtol               = 1e-05
optimize_fft             = yes
fourierspacing           = 0.15

2)If I solvate the system with tip4p, I can do minimization (although ending
very early) and I can perform POSRE NVT equilibration. When I switch to NVT w/o
restrains on the peptide, system gives out LINCS errors (relative constraint
deviation) although I dont use any constraints. I also turned off PME. 

I saw some emails talking about tip4p constraints. But I am clueless about in
vacuo.
any help appreciated.
Murat CETINKAYA, M.Sc.
BioNanoMaterials Group,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176