Moeed wrote:
Dear Justin,
The actual box I got by replicating monomer units has size of 15 0.5
0.5!!!! That is chain has no space to move. I know you have already
given me some tips on high repulsion in the system but that had to do
with incorrect topology file. I assure you I have learned a lot from
your tips ;)
I'm glad to hear it. The same principal still applies, though. If a large
system is failing, break it down into manageable pieces to determine where
things start to break down. It is easier to solve one problem at a time than
several.
This time I need to have such packed system because that gives me the
density I want. 0.9g/cm3 for PE! for a chain of 60 ethylene units the
size should be identical to the actual size 15 0.5 0.5. And I am
wondering how can I work with much longer chains ( 20 times longer)...
You've been given advice about this. You probably will have to simulate within
a larger box and slowly compress your system. You have constructed a linear
chain of PE within a pre-defined box that gives you the density you want. Ask
yourself this: is that what PE looks like, completely rigid and extended?
Certainly not. The better approach would be as Vitaly and Chris have suggested
- take a single molecule of PE in a very large box (forget your density for a
moment) and simulate it. It will probably adopt a much more reasonable
structure that you can then work with. Then slowly build up your system - 2, 4,
8 units - and it will likely be far more stable. If your box fits your system
exactly, your atoms will be extremely close to one another and you will get a
huge vdW repulsion. If you've learned anything from me, you should already know
that I want you to break down your energy terms to see what's failing...
md grompp is giving error about degrees of freedom. Any advise on this
in appreciated...
Thank you,
md
grompp****************************************************************************
aking dummy/rest group for Acceleration containing 2896 elements
Making dummy/rest group for Freeze containing 2896 elements
Making dummy/rest group for Energy Mon. containing 2896 elements
Making dummy/rest group for VCM containing 2896 elements
Number of degrees of freedom in T-Coupling group Eth is 5373.22
Number of degrees of freedom in T-Coupling group EthB is 211.89
Number of degrees of freedom in T-Coupling group EthE is 211.89
Making dummy/rest group for User1 containing 2896 elements
Making dummy/rest group for User2 containing 2896 elements
Making dummy/rest group for XTC containing 2896 elements
Making dummy/rest group for Or. Res. Fit containing 2896 elements
Making dummy/rest group for QMMM containing 2896 elements
T-Coupling has 3 element(s): Eth EthB EthE
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
There is no error message here. What's the problem?
mdpfile**************************************************************************************
title = PE-Hexane
;define = -DPOSRES ; tells gromacs to perform
position restrained dynamics/include posre.itp into topology used for
position restraint
pbc = xyz ; use priodic BCs in all
directions
; Run control
integrator = md ; type of dynamics algorithm.
Here md uses a leap-frog algorithm for integrating Newtons's eq of motion
dt = 0.002 ; in ps !
nsteps = 5000 ; length of simulation= nsteps*dt
nstcomm = 1 ; frequency for center of mass
motion removal
; Output control
nstenergy = 100 ; frequency to write energies to
energy file. i.e., energies and other statistical data are stored every
10 steps
nstxout = 100 ; frequency to write
coordinates/velocity/force to output trajectory file. how often
snapshots are collected= nstxout*dt
nstvout = 100
nstfout = 0
nstlog = 100 ; frequency to write energies to
log file
nstxtcout = 10 ; frequency to write coordinates
to xtc trajectory
; Neighbor searching
nstlist = 10 ; frequency to update neighbor
list. Neighborlist will be updated at least every 10 steps. Manual p80
ns_type = grid ; make a grid in the box and
only check atoms in neighboring grid cells when constructing a new
neighbor list every nstlist steps
; Electrostatics/VdW
coulombtype = Shift ; tells gromacs how to model
electrostatics. Coulomb/LJ potential is decreased over the whole range
and forces decay smoothly to zero betw$
vdw-type = Shift ; rcoulomb-switch/rvw-switch &
rcoulomb/rvdw
rcoulomb-switch = 0 ; where to start switching the
Coulomb potential
rvw-switch = 0 ; where to start switching the
LJ potential
; Cut-offs
rlist = 1.1 ; in nm. Cut-off distance for
short-range neighbor list
rcoulomb = 1.0 ; distance for coulomb cut-off
rvdw = 1.0 ; distance for coulomb cut-off
; Temperature coupling
Tcoupl = berendsen
tc-grps = Eth EthB EthE ;HEX ; groups to
OK, this is a terrible idea. You've broken down a bonded molecule into pieces,
something that is completely unphysical. Imagine if we coupled individual amino
acids of a protein separately...
I'll assume this is the source of your error message, but if that's not the
case, please be sure to actually provide all the relevant information.
-Justin
--
========================================
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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