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<DIV><FONT face=Arial size=2> Regarding the crash when doing MD
after EM, try to look at the output log, you will see the number of the atom
which probably make problems e.g. atom #200 at:</FONT></DIV>
<DIV><FONT face=Arial size=2>Step= 533, Dmax= 2.5e-03 nm, Epot=
-3.51631e+05 Fmax= 2.02906e+03, atom= 200</FONT></DIV>
<DIV><FONT face=Arial size=2>try to look at it using VMD or SpdbViewer
etc.</FONT></DIV>
<DIV><FONT face=Arial size=2>Regarding the question about grouping the residues,
you can use make_ndx to index the three residue into one group.</FONT></DIV>
<DIV><FONT face=Arial size=2>About the different chains, try to put letters as
index instead of using <FONT face="Times New Roman" size=3>MODEL-TER-ENDMDL, it
should work.</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<BLOCKQUOTE dir=ltr
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=obrien@CLEMSON.EDU href="mailto:obrien@CLEMSON.EDU">Chris O'Brien</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Tuesday, February 24, 2004 5:29
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] mdrun failure plus
other questions</DIV>
<DIV><BR></DIV>Dear gmx-users,<BR><BR>I am having trouble getting an mdrun to
start successfully. My system is a periodic box containing 20
polylactide 50-mers of the residue form SL1-(SL2)n-SL3. Prior to an
mdrun, I minimized the system with cg to Epot = -5.1736e4 and Fmax =
0.979. My grompp command line for the input to the mdrun includes the
*.gro and the *.trr file from the output of the final minimization.
However, when I try an mdrun, the system behaves as if there are very large
forces present: I get LJ (SR) values of 1e10, "1-4 interactions at a distance
greater than 1" warnings to screen and "1-4 interaction not within cutoff" in
the -debug file, the temperature and pressure increase to the order of 1e18,
and everything goes "nan". Also, it says "Large VCM (group rest):
-0.0000,<X-TAB> </X-TAB>-0.0000, -0.0000. How is
(negative) zero large?<BR><BR>I have tried changing several parameters to see
if it would help, to no avail. Here is a representative mdp file for the
simulations after I had turned off the T and P coupling.<BR><BR><FONT
face="Courier New, Courier"
size=2>define
=
<BR>integrator
=
md<BR>dt
= 0.0005
;ps<BR>nsteps
= 10000 ;
<BR>nstcomm<X-TAB> </X-TAB><X-TAB> </X-TAB>
=
+1<BR>nstxout
=
5000<BR>nstvout
=
5000<BR>nstlog
=
5000<BR>nstenergy
=
5000<BR>nstfout<X-TAB> </X-TAB><X-TAB> </X-TAB>
=
5000<BR>nstxtcout
=
5000<BR>;xtc_grps
=
SL1<X-TAB> </X-TAB>SL2<X-TAB> </X-TAB>SL3<BR>energygrps
= SL1 SL2
SL3<BR>nstlist
=
5<BR>ns_type
=
grid<BR>pbc<X-TAB> </X-TAB><X-TAB> </X-TAB><X-TAB> </X-TAB>
=
xyz<BR>rlist
=
1.0<BR>coulombtype
=
cut-off<BR>rcoulomb
=
1.0<BR>vdwtype<X-TAB> </X-TAB><X-TAB> </X-TAB>
=
cut-off<BR>rvdw
=
1.0<BR>tcoupl
=
no;berendsen<BR>tc-grps
= SL1 SL2
SL3<BR>tau_t
= 0.1 0.1
0.1<BR>ref_t
= 300 300
300<BR>Pcoupl
=
no;berendsen<BR>pcoupltype<X-TAB> </X-TAB><X-TAB> </X-TAB>
= isotropic
<BR>tau_p
= 2.0<BR>compressibility
=
4.5e-5<BR>ref_p
=
1.0<BR>gen_vel
=
yes<BR>gen_temp
=
50<BR>gen_seed
=
173529<BR>constraints
= none<BR><BR></FONT>The box is a 20 nm cube, so the molecules aren't seeing
their duplicates. <BR><BR>A few somewhat related topics that this
question brought to mind:<BR><BR>1. I don't think I really need to couple or
record separately for each residue. How do I declare this in the
mdp? With "system", "Protein", or something else?<BR><BR>2. Although the
pdb file used to make the system includes 20 distinct polymer chains, the
*.top file lists only a single molecule (Protein). Is this
problematic? Pdb2gmx wouldn't run if I didn't remove the
MODEL-TER-ENDMDL lines from the pdb file. With smaller systems, I can
work around this with chain identifiers, but that doesn't work so well when
the size and number of polymers gets large, and I would rather have a single
*.top file than multiple *.itp files.<BR><BR>My apologies for the jumble of
questions, and I look forward to any input people might have.<BR><BR>Thank
you,<BR><BR>Chris O'Brien<BR><X-SIGSEP>
<P></X-SIGSEP>Department of Chemical Engineering<BR>Clemson
University<BR>Clemson, SC 29634-0909<BR></P></BLOCKQUOTE></BODY></HTML>