<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Well, there must be some thing some where that you did the wrong way :)) <div><br></div><div>You should try again from the start and may be try to post on the Martini website forum </div><div><a href="http://www.cgmartini.nl">www.cgmartini.nl</a></div><div><br></div><div>XAvier</div><div><br><div><div>On Jun 20, 2011, at 9:41 AM, Naba wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></div></body></html>