<FONT size=2> <div>Dear gmx users,</div> <div> I downloaded POPE.itp and lipid.itp files from Dr.Tieleman website <A href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</A> and POPG.itp file from Dr.Mikko Karttunen wesite <A href="http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml">http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml</A>.</div> <div>I built a POPE:POPG bilayer in 3:1 ratio. When I am minimizing the bilayer, bonds in head groups are breaking in POPE and POPG lipid molecules.</div> <div> </div> <div>Here is my min.mdp input file</div> <div> </div> <div>cpp = /lib/cpp</div> <div>define = -DFLEXIBLE</div> <div>constraints = none</div> <div>integrator = steep</div> <div>nsteps = 2000</div> <div>;</div> <div>; Energy minimizing stuff</div>
<div>;</div> <div>emtol = 100</div> <div>emstep = 0.01</div> <div>nstcomm = 1</div> <div>ns_type = grid</div> <div>rlist = 1</div> <div>rcoulomb = 1.0</div> <div>rvdw = 1.0</div> <div>Tcoupl = no</div> <div>Pcoupl = no</div> <div>gen_vel = no</div> <div>xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx </div> <div> </div> <div>while creating *.tpr file using the above file for minimization, I am getting fallowing message.............</div> <div> </div> <div></div> <div>calling /lib/cpp...</div> <div>In file included from pg-pe.top:5:</div> <div>dpopg.itp:10:8: warning: multi-line string literals are deprecated</div> <div>processing topology...</div> <div>Generated 344865 of the 344865 non-bonded parameter combinations</div> <div>Generating 1-4 interactions: fudge = 0.5</div> <div>Generated 344775 of the 344865 1-4 parameter combinations</div> <div>Excluding 3 bonded neighbours for POP 48</div> <div>Excluding 3 bonded neighbours for DPO
16</div> <div>Excluding 2 bonded neighbours for SOL 2481</div> <div>NOTE:</div> <div>System has non-zero total charge: -1.599999e+01</div> <div></div> <div>processing coordinates...</div> <div>double-checking input for internal consistency...</div> <div>renumbering atomtypes...</div> <div>converting bonded parameters...</div> <div># BONDS: 8242</div> <div># ANGLES: 6257</div> <div># PDIHS: 1712</div> <div># RBDIHS: 1472</div> <div># IDIHS: 272</div> <div># LJ14: 1840</div> <div>initialising group options...</div> <div>processing index file...</div> <div>Making dummy/rest group for T-Coupling containing 10787 elements</div> <div>Making dummy/rest group for Acceleration containing 10787 elements</div> <div>Making dummy/rest group for Freeze containing 10787 elements</div> <div>Making dummy/rest group for Energy Mon. containing 10787 elements</div> <div>Making dummy/rest group for VCM containing 10787 elements</div> <div>Number of degrees of freedom in
T-Coupling group rest is 32358.00</div> <div>Making dummy/rest group for User1 containing 10787 elements</div> <div>Making dummy/rest group for User2 containing 10787 elements</div> <div>Making dummy/rest group for XTC containing 10787 elements</div> <div>Making dummy/rest group for Or. Res. Fit containing 10787 elements</div> <div>Making dummy/rest group for QMMM containing 10787 elements</div> <div>T-Coupling has 1 element(s): rest</div> <div>Energy Mon. has 1 element(s): rest</div> <div>Acceleration has 1 element(s): rest</div> <div>Freeze has 1 element(s): rest</div> <div>User1 has 1 element(s): rest</div> <div>User2 has 1 element(s): rest</div> <div>VCM has 1 element(s): rest</div> <div>XTC has 1 element(s): rest</div> <div>Or. Res. Fit has 1 element(s): rest</div> <div>QMMM has 1 element(s): rest</div> <div>Checking consistency between energy and charge groups...</div> <div>writing run input file...</div>
<div>xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</div> <div> </div> <div>My question,</div> <div>Why bonds are breaking in POPG and POPE lipid molecules. </div> <div>Any suggestion is appreciated.</div> <div> Thank you in advance.</div> <div> with regards,</div>
<div> Nagaraju Mulpuri.</div> <div> </div> <div> </div></FONT><p> 
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