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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