<p>Hi Folks,</p>I was trying to make a large POPC system from Tieleman's 128 lipid assembly.
Everything went well until I tried to run dynamics. While trying to run
dynamics, I got a large velocity for the center of mass (Large VCM) error. The
log file, mdp file, and the top file are attached as a suse .zip<br>
<div> </div>
<div>Here is what I did:</div>
<p>- replicated the system thrice to make is 512 lipids (this was done in VMD),
and translated replicas along the bilayer plane accordingly</p>
<p>- to remove bad contacts, minimized it in GROMACS (steep minimization)</p>
<p>- to remove bad contacts farther, minimized using CG</p>
<div>
<div>(The system looks fairly reasonable after minimization on visual
inspection)</div></div>
<div> </div>
<div>- tried to assign velocities at 50 K and run NPT dynamics, with water
molecules constrained along the bilayer normal (z)</div>
<div> </div>
<div>In the last step, the system crashes after a few hundred steps, reporting a
large VCM. A look at the pdb files reveals that the system is exploding with
large vacuum regions appearing. </div>
<div> </div>
<div>THE BOX CENTER WAS VERY FAR FROM THE GEOMETRIC ORIGIN. The box is ~ 13 x
13 x 6.7, and the center is at 6.3, 6.3, 3.5. So I also tried the following
before running dynamics:</div>
<p>- used editconf -c to center the box, before running dynamics. But this only moved the center by less than 5 angstroms. Why ? <br>- used
editconf -c -center 0 0 0 as a variant of the above.</p><p>The above did not solve the problem.<br></p>
<div>Please let me know if you want me to send you more details ?</div>
<div> </div>
<div>Thanks for the help,</div>
<p>-Himanshu</p>MEMPHYS,<br>SDU, Denmark