On 6/27/12 7:36 AM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am using gromacs version 4.5.5. , while running grompp (for any
purpose i.e. minimization , equilibration etc. )
I am getting following screen output without any warning, error or
note relevant to it.
"Generated 830 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_B'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL' "
My question is whether to ignore or consider this as an error ?
This output is perfectly normal, and is (or at least, should be) present for any
system that has more than monoatomic species.
I really don't know why this screen output is coming which I never
faced ? Is there any mistake by me ? Please suggest .
There is no mistake. Please refer to the manual, section 4.6.1.
-Justin
cg.mdp for reference
; Conjugate Minimization
; Protein - Water - Ligand ( all free to move)
;
;
;
Title = Pro-Lig H2O
define = -DFLEXIBLE ; specifies flexible water
constraints = none
integrator = cg
nsteps = 2000
ns_type = grid
rlist = 1.2
coulombtype = pme
vdw-type = cut-off
rvdw = 1.2
rcoulomb = 1.2
;
; Energy Minimization Stuff
;
;
emtol = 0.0000001
emstep = 0.01
Thanking you in advance .
Regards,
Pavan Payghan
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
