<div>Hi Michael,</div>
<div> </div>
<div>are you simulating with a constant area, volume or pressure ensemble?<br>If you are using the configuration you mention as a starting point and simulating it with another forcefield, as Mark pointed out, it's not unexpected to find problems.
</div>
<div>Moreover, equilibration in lipid simulations... takes time!! At least 10-20 ns of simulation, as a rough estimate. </div>
<div>If you are using constant area or volume, observe that a DPPC bilayer has an experimental area per lipid of 64 A**2 at 50 C, so you should start with this value.</div>
<div>Regarding constant pressure simulations, your system must reach that value.</div>
<div> </div>
<div>Regards.</div>
<div> </div>
<div>Pedro. </div>
<div> </div>
<div><br> </div>
<div><span class="gmail_quote">2007/4/6, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Michael Skaug wrote:<br>> I am trying to perform a simulation of 128 dppc in 3655 spc water.<br>> I obtained .pdb and .top files from the Biocomputing website at
U.Calgary.<br>> I do nothing to alter the structure, which must be minimized as it comes<br><br>err, not minimized - sampled from the ensemble they were using, which<br>needn't correspond to the ensemble you're using. As soon as you generate
<br>new velocities, the source of your structure will only give you the same<br>gross morphology, not an equilibrated system.<br><br>> from the end of a 1 ns simulation. Processing the input files works fine,<br>> but the mdrun always ends somewhere between step 500 and step 3000. I have
<br>> tried adjusting various parameters, such at the time step, tau_p, tau_t and<br>> the compressibility, but nothing has created a consistent run.<br>> I wonder where I should be focusing my time to solve this problem. Should
<br>> I focus on the parameters and structure, or computer hardware/software?<br><br>We can't tell unless you tell us what GROMACS is reporting as the problem.<br>_______________________________________________<br>
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