<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi<div><br></div><div>1) I am using Amber03 forcefield.</div><div><br></div><div>2) In most cases Yes, but in others, implicit solvent simulations tend to crash almost immediately (after reporting segmentation fault).</div><div><br><div><div>3) It generally takes less than a couple of 100 ps for the loss of the secondary structure. A few times, I even received .gro files at the end with all values as "nan".</div><div><br></div><div>Earlier I thought it might be a problem with equilibration, but I have tried to run energy-minimization more than once followed by position-restrained runs as well (to equilibrate H-atoms). But the end result hasn't changed. </div><div><br></div><div>Thanks & Regards</div><div>Kush</div><div> </div><div><br></div><div><br></div>-----------------------------------------------------------------------------------</div><div><meta charset="utf-8"><span class="Apple-style-span" style="font-family: Times; "><b>Michael Shirts:</b></span></div><div><meta charset="utf-8"><span class="Apple-style-span" style="font-family: Times; "><pre>A few questions:
1) What force field are you using?
2) do you get the same answers with and without GPU acceleration?
3) How long does it take for secondary structure to disappear? 100's
of ps? 10's of ns?
</pre><div><br></div></span></div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br class="Apple-interchange-newline"><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">--</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Kushagra Singhal<br>Promovendus, Computational Chemistry<br>van 't Hoff Institute of Molecular Sciences<br>Science Park 904, room C2.119<br>1098 XH Amsterdam, The Netherlands<br>+31 205256965<br>Universiteit van Amsterdam<br><a href="mailto:k.singhal@uva.nl">k.singhal@uva.nl</a><br><br></div></span>
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