<span style="font-family: verdana,sans-serif;">Dear Users/Developers</span><br style="font-family: verdana,sans-serif;"><br style="font-family: verdana,sans-serif;"><span style="font-family: verdana,sans-serif;">I am trying to set a coarse-grained MD for the same protein (1UBQ.pdb) therein the MARTINI tutorial (<a href="http://md.chem.rug.nl/cgmartini/index.php/tutorial">http://md.chem.rug.nl/cgmartini/index.php/tutorial</a>).</span><br style="font-family: verdana,sans-serif;">
<span style="font-family: verdana,sans-serif;">After the solvation by water-1bar-303K.gro I tried to minimize the system but it gives the following weired results.</span><br style="font-family: verdana,sans-serif;"><br style="font-family: verdana,sans-serif;">
<span style="font-family: verdana,sans-serif;">grompp gives the following output:</span><br><br>checking input for internal consistency...<br>processing topology...<br>Generated 0 of the 465 non-bonded parameter combinations<br>
Excluding 1 bonded neighbours molecule type 'Protein'<br>Excluding 1 bonded neighbours molecule type 'W'<br>processing coordinates...<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>
converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>There are: 76 Protein residues<br>There are: 5199 Other residues<br>Analysing Protein...<br>
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>Making dummy/rest group for T-Coupling containing 5362 elements<br>Making dummy/rest group for Acceleration containing 5362 elements<br>
Making dummy/rest group for Freeze containing 5362 elements<br>Making dummy/rest group for Energy Mon. containing 5362 elements<br>Making dummy/rest group for VCM containing 5362 elements<br>Number of degrees of freedom in T-Coupling group rest is 16053.00<br>
Making dummy/rest group for User1 containing 5362 elements<br>Making dummy/rest group for User2 containing 5362 elements<br>Making dummy/rest group for XTC containing 5362 elements<br>Making dummy/rest group for Or. Res. Fit containing 5362 elements<br>
Making dummy/rest group for QMMM containing 5362 elements<br>T-Coupling has 1 element(s): rest<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>
User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>
Checking consistency between energy and charge groups...<br>This run will generate roughly 2 Mb of data<br>writing run input file...<br><br><span style="font-family: verdana,sans-serif;">But mdrun gives the following output:</span><br>
<br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+00<br> Number of steps = 5000<br>Step= 14, Dmax= 1.2e-06 nm, Epot= 3.55783e+18 Fmax= inf, atom= 294<br>Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>but not to the requested precision Fmax < 1<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br>
<br>writing lowest energy coordinates.<br><br>Back Off! I just backed up solvated.gro to ./#solvated.gro.1#<br><br>Steepest Descents converged to machine precision in 15 steps,<br>but did not reach the requested Fmax < 1.<br>
Potential Energy = 3.5578291e+18<br>Maximum force = inf on atom 294<br>Norm of force = 1.0627526e+19<br><br style="font-family: verdana,sans-serif;"><span style="font-family: verdana,sans-serif;">Maximum force is equal to infinity and hence I am afraid to proceed further. Can someone help me out? </span> <br>
<br><br style="font-family: verdana,sans-serif;" clear="all"><span style="font-family: verdana,sans-serif;">Thanks in advance.</span><br><br><font color="#888888">Nabajyoti Goswami<br><br>Senior Research Fellow<br>Bioinformatics Center, Sri Venkateswara College<br>
University of Delhi South Campus<br>Benito Juarez Road, Dhaula Kuan<br>New Delhi 110021<br>India</font><br><br>