[gmx-users] Problem in followin MARTINI tutorial

[XAvier Periole]

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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