On 1/5/13 8:45 PM, Xu Dong Huang wrote:
for some reason my message is too long and held for approval, but anyway,
Starting Energy Minimized structure:
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png
Ending NVT outcome .gro structure:
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83509PM_zpsb4f658b2.png
@Justin, this is the same star polymer you've seen before, and I assume you
were aware that there is a definite bond interaction definition and etc. (So I
don't think the structure should have blown up like that)
MDP information:
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 100000
nstcomm = 1
comm-grps =
nstxout = 100
nstvout = 100
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 0
xtc_precision = 1000
xtc-grps =
energygrps = system
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = V-rescale
tc-grps = system
tau_t = 1.0
ref_t = 300
Pcoupl = no
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
The topology is the same one from last time I sent you, a star. bond order
defined. (Can't attach it on here because it's too long and my message will be
held for approval by gmx)
The topology is the most important bit of information. Please post a link where
it can be downloaded. What are your box vectors? What is the minimum
box-solute distance?
-Justin
--
========================================
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
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