<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear all,<br>
I created .gro and .top files for my structure with
48 repeat units of polymer surrounded by sodium ions and water. First I
carried out energy minimization by steepest descents and then I ran MD
for 2ps (40 steps). It runs upto 40 steps properly and then it
starts giving errors as follows:<br>
<font size="1">starting mdrun 'Protein'<br>
1000 steps, 2.0 ps.<br>
<br>
step 40, remaining runtime: 23
s
Warning: 1-4 interaction between 294 and 297 at distance larger than 1
nm<br>
These are ignored for the rest of the simulation<br>
turn on -debug for more information<br>
step 50, remaining runtime: 18
s
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Back Off! I just backed up step55.pdb to ./#step55.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Back Off! I just backed up step56.pdb to ./#step56.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
...<br>
Back Off! I just backed up step60.pdb to ./#step60.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
Fatal error: ci = -2147483648 should be in 0 .. 1330 [FILE nsgrid.c, LINE 218]<br>
<br>
<font size="3">Also when I ran steepest desc<font size="1"><font size="3">ents the messages I got were as follows:<br>
<br>
</font>Step= 44, Dmax= 1.2e-04 nm, Epot= -1.10077e+05 Fmax= 2.65510e+03, atom= 725<br>
Step= 52, Dmax= 1.1e-06 nm, Epot= -1.10077e+05 Fmax= 3.00823e+03, atom= 8860<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 1000<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 steep.trr to ./#steep.trr.1#<br>
<br>
Back Off! I just backed up steepout.gro to ./#steepout.gro.1#<br>
<br>
Steepest Descents converged to machine precision in 53 steps,<br>
but did not reach the requested Fmax < 1000.<br>
Potential Energy = -1.1007694e+05<br>
Maximum force = 2.6551050e+03 on atom 725<br>
Norm of force = 1.0160128e+05</font><br>
<br>
Where am I going wrong? Please tell me. Thanking you in advance.<br>
<br>
Rahul Karyappa<br>
NCL, Pune </font><br>
</font><br>
<br>
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