Nilesh Dhumal wrote:
I used the opls parameters in gromacs.
...and what parameters would those be? I don't know of any "standard" glucose
parameters that are included in the Gromacs distribution, at least not for OPLS-AA.
Also, what was the outcome of energy minimization? Did it converge? Did it
crash? Why are you using such a large emstep? I suspect that 0.1 may lead to
instability.
-Justin
NIlesh
On Thu, May 27, 2010 1:17 pm, Erik Marklund wrote:
Where did you get the parameters for glucose? Those are my first
suspects.
Erik
Nilesh Dhumal skrev:
After energy minimzation, I visualized the pdb and all atoms are really
far from each other.
NIlesh
On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:
Bonds don't break in gromacs without qm/mm ...yet. Why do you think
they're broken?
Erik
Nilesh Dhumal skrev:
Hello,
I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization, I found all the
bonds are broken. I have pasted the input file for energy
minimzation. WHy all bonds are geting broken.
Nilesh
define = -DFLEXIBLE
constraints = all-bonds
integrator = L-BFGS
nsteps = 15000
nbfgscorr = 50
emtol = .001
emstep = 0.1
gen_vel = yes
gen-temp = 300
nstcomm = 1
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist =10
; ns algorithm (simple or grid)
ns-type = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = no
; nblist cut-off
rlist = 0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-Off
rcoulomb-switch = 0
rcoulomb = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
; Method for doing Van der Waals
vdw-type = Cut-off
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = no
; nblist cut-off
rlist = 0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-Off
rcoulomb-switch = 0
rcoulomb = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
; Method for doing Van der Waals
vdw-type = Cut-off
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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