My protein complex was minimized initially before putting into the lipid. POPC is also a preequilibrated structure from Tielemen website. I don't quite understand on what you meant by "the protein is not happy with the restraint". The system went well through out the nvt, npt with restraint on protein.... Once it move to md production run ( which is without restraint on protein), error occurred (range checking error). <br>
The reason i'm using the version3.3.2 is because the forcefield i'm using at the moment only support version3.3.2. Is my problem cause by bug of the older version? is there any bugfix fot this? please<br>help.<br>
<br>regards,<br>Bing<br><br>
<br><div class="gmail_quote">On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Bing Bing wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All,<br>
I'm running the protein complex with POPC system. NVT (100ps) and NPT (200ps) were done with restraint on the protein follow by 1000 ps of NPT without restraint on protein. The trajectory was checked in term of pressure, potential, area per lipid ....were checked and everything seems ok (potential almost plateu, area per lipid close to experimental value). I proceeded with md (similar to Justin's tutorial) for 1 ns. The simulation stop around 800ps with the range checking error.<br>
</blockquote>
<br></div>
OK so look at the collective variables, and/or trajectory to find evidence of the problem. The most likely explanation is that your protein was unhappy in the restraints, of course. Perhaps you should try some vacuum EM before you embed it in the lipid, or some such.<div>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I'm using gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired to be more gentle while releasing the restraint.Different stepwise of releasing the restraint during NPT were tried and followed by production MD, all the simulation stop or i shall said it crashed around ~800ps with the same error (range checking error). I'm out of idea what is the problem here. Please advice.<br>
</blockquote>
<br></div>
Range checking is just one of many things that can be the first thing to break when there's an underlying systemic problem.<br>
<br>
Also, unless you need scientific continuity, 3.3.2 is about 4 years old... 4.0.5 will be much faster!<br>
<br>
Mark<br>
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