<pre>>><i> I am trying to simulate my own structure based simulation using 3.3.2.<br></i><br>>What sort of structure?<br>RNA with a ligand (the ligand is the trouble)<br><br>>><i> I<br></i>>><i> have developed the forcefield and it works fine without periodic boundary
<br><br></i>><i><span style="font-style: italic;">></span> conditions. When I use pbc=xyz atoms that are connected in the [bonds]<br></i>><i><span style="font-style: italic;">></span> section of the topology get broken. What happens is 1 of the two atoms
<br><br></i>><i><span style="font-style: italic;">></span> will<br></i>><i><span style="font-style: italic;">></span> cross the boundary and that single atom will get placed on the opposite</i><i><span style="font-style: italic;">
<br>>></span> side<br></i>><i><span style="font-style: italic;">></span> of the box.<br></i><br>>This won't be the source of the problem, unless they broke PBC in 3.3.2<br>>and you're the first to notice :-)
<br><br><br><br>I should clarify. At 1 step, the atom gets moved from 1 side of the box to the other. <br>In the following step, the entire molecule gets "ripped to pieces". It appears that lincs<br>is trying to satisfy the constraints, so the whole molecule gets move "near" the center. It
<br><br><br>is near in that it is no longer close to the side of the box, but the individual atoms are still <br>quite a distance apart (~20 Angstroms). <br><br><br>>><i> In the next step, the system will explode. If I use lincs, I
<br><br></i>><i>> get error messages about angles getting changed and that lincs can not<br></i>><i><span style="font-style: italic;">><br></span> satisfy the constraint. I get the same issue with shake. when i run
<br><br><br></i>><i><span style="font-style: italic;">></span> lincs,<br></i>><i><span style="font-style: italic;">></span> the structure is output before the errors and after, so I can see that 1<br><br></i>>
<i><br>> atom is placed on the opposite side of the box and that is the same atom<br></i>><i><span style="font-style: italic;">></span> that I get lincs errors about. Below is my .mdp file.<br><br></i><br><br>>You don't mention your EM or equilibration regime. Please use one, or
<br><br>>describe yours :-)<br><a href="http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"><br>http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
<br><br></a><br>I run minimization and that works, IF none of the atoms cross the border. If I make my box a little smaller,<br>such that atoms are over the boundaries initially, then I get the same errors with lincs. If I use a larger box, and
<br><br>minimize, I can start the run juts fine. The simulations runs ok for about 16,000 time steps, and then the <br>problem surfaces. If I use the cvs version, I get the message<br><br>There were 6 inconsistent shifts. Check your topology
<br><br> Energies (kJ/mol)<br> Bond Angle Proper Dih. Improper Dih. LJ-14<br> 6.62576e+06 1.09907e+03 2.71644e+02 2.49075e+02 -1.13891e+03<br> Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.
<br><br> 0.00000e+00 3.58079e+00 0.00000e+00 6.62624e+06 4.66262e+04<br> Total Energy Temperature Pressure (bar)<br> 6.67287e+06 1.10673e+03 -2.18054e+04<br><br>There were 2 inconsistent shifts. Check your topology
<br><br> Step Time Lambda<br> 11400 5.70000 0.00000<br><br>There were 22 inconsistent shifts. Check your topology<br>-------------------------------------------------------
<br><br>Program mdrun, VERSION 3.3.1<br>Source code file: stat.c, line: 257<br><br>Fatal error:<br>XTC error<br>-------------------------------------------------------<br><br>"You Hear Footsteps Coming From Behind" (Colossal Cave)
<br><br>If I use 3.3.1 I get the following message (immediately) when I try to run the system<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 3.3.1<br>Source code file: mshift.c, line: 91
<br><br>Fatal error:<br>More than 8 graph edges per atom (atom 432)<br><br>-------------------------------------------------------<br><br>"It Costs Too Much If It Costs a Lot" (Magnapop)<br><br><br><br>>><i>
I saw the same errors have been posted when people try to run infinite<br></i>><i>> polymers, but I didn't see any resolution to this. Any help would be<br></i>><i>> appreciated. thanks<br><br></i><br>>Does the same problem occur for a different part of your system if you
<br>>change the seed for generating velocities?<br><br>I haven't tried different seeds, but I have done runs at different temperatures<br>and, I get the same errors, once the molecule hits the boundaries.<br><br>Perhaps these issues with other versions can make it obvious what is going on.
<br><br>>Mark</pre>