[gmx-users] number of degrees of frredom
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 12 17:46:27 CEST 2010
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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