Hi all,
<div><br></div><div>I've been working on some structures between 2.5A and 3.4A in resolution and all of my structures suffer from lincs warnings.</div><div>From reading the page about lincs warnings, I've performed a more lengthy equilibration:</div>
<div><br></div><div>I'm using gromacs 4.0.7 single precision and the G53a6 force field with spc water model.</div><div><br></div><div>- Genbox, add ions.</div><div>- EM until converges</div><div>- Positional restraints at 2,000 kJ/mol, 200, 20 and 2 for 100ps each at 100K</div>
<div>- Followed by simulated annealing with the following parameters:</div><div><br></div><div><div>; Simulated annealing @ positional restraint of 2 kJ/mol</div><div>annealing <span class="Apple-tab-span" style="white-space:pre"> </span>= single single</div>
<div>annealing_npoints <span class="Apple-tab-span" style="white-space:pre"> </span>= 3 3</div><div>annealing_time <span class="Apple-tab-span" style="white-space:pre"> </span>= 0 50 250 0 50 250</div><div>
annealing_temp<span class="Apple-tab-span" style="white-space:pre"> </span>= 100 100 300 100 100 300</div></div><div><br></div><div>- This then undergoes 750ps of md at 300K.</div><div><br></div><div>Once done. I continue the run in my production MD.</div>
<div>Sometimes my structures will crash within 5 ns, sometimes it will run out for 60 ns before I start seeing any lincs warnings.</div><div><br></div><div>I've attempted to further refine the structures and they behave a little better, but still crash, just less often.</div>
<div>To continue the simulation, I will not use the .trr output from the previous simulation. If this doesn't work, I'll run the simulation using shake for 2 ns, but this is significantly slower.</div><div><br></div>
<div>I'm a little concerned that these crashes may be introducing some sort of error into the simulation and I'm not sure of the right way to get around this problem.</div><div>I've played around with changing the lincs order and lincs iteration parameters, which appear to reduce the number of lincs warnings and slows down the simulation slightly.</div>
<div><br></div><div>Another thing I've played with was the constraints. Changing this from all-bonds to hbonds.</div><div>This stopped my crashes, but a co-worker thought that it may not be accurately modelling the system, or would introduce anomalies into the simulation.</div>
<div>My impression was that changing from all-bonds to hbonds would improve the accuracy of the system... But I could be wrong.</div><div><br></div><div>If anyone has experience with dealing with lincs warnings or simulating low resolution structures, help would be amazing.</div>
<div>I've been stuck on this for quite some time now.</div><div><br></div><div><br></div><div>Cheers, Ben</div>