Well, there must be some thing some where that you did the wrong way :))
You should try again from the start and may be try to post on the
Martini website forum
www.cgmartini.nl
XAvier
On Jun 20, 2011, at 9:41 AM, Naba wrote:
Dear Users/Developers
I am trying to set a coarse-grained MD for the same protein
(1UBQ.pdb) therein the MARTINI tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial
).
After the solvation by water-1bar-303K.gro I tried to minimize the
system but it gives the following weired results.
grompp gives the following output:
checking input for internal consistency...
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are: 76 Protein residues
There are: 5199 Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...
Making dummy/rest group for T-Coupling containing 5362 elements
Making dummy/rest group for Acceleration containing 5362 elements
Making dummy/rest group for Freeze containing 5362 elements
Making dummy/rest group for Energy Mon. containing 5362 elements
Making dummy/rest group for VCM containing 5362 elements
Number of degrees of freedom in T-Coupling group rest is 16053.00
Making dummy/rest group for User1 containing 5362 elements
Making dummy/rest group for User2 containing 5362 elements
Making dummy/rest group for XTC containing 5362 elements
Making dummy/rest group for Or. Res. Fit containing 5362 elements
Making dummy/rest group for QMMM containing 5362 elements
T-Coupling has 1 element(s): rest
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
Checking consistency between energy and charge groups...
This run will generate roughly 2 Mb of data
writing run input file...
But mdrun gives the following output:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 5000
Step= 14, Dmax= 1.2e-06 nm, Epot= 3.55783e+18 Fmax= inf,
atom= 294
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up solvated.gro to ./#solvated.gro.1#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 3.5578291e+18
Maximum force = inf on atom 294
Norm of force = 1.0627526e+19
Maximum force is equal to infinity and hence I am afraid to proceed
further. Can someone help me out?
Thanks in advance.
Nabajyoti Goswami
Senior Research Fellow
Bioinformatics Center, Sri Venkateswara College
University of Delhi South Campus
Benito Juarez Road, Dhaula Kuan
New Delhi 110021
India
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