<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sopna,<div><br></div><div>First, can you attached the crash report of GROMACS 4.5, so we can have a look on it? Second, are you doing EM and PR before you run it using 4.5? Even if you transfer a stable system from 4.0 it might need some equilibration before you actually run MD, specifically if you assign new velocities to atoms.</div><div><br></div><div>Cheers,</div><div>Itamar</div><div><br></div><div><div>On 20/10/2011, at 8:40 AM, Sapna Sarupria wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello,<div><br></div><div>I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5 are still crashing in 4.5.4. I think it is related to constraints but I am unable to figure out exactly what is different. I have pasted both my topology and mdp (updated for 4.5.4) files. Any ideas? I have read through the manual and it seems like the mdp files does not need any changes, but perhaps I am missing something.</div>
<div><br></div><div>Thank you for your help!</div><div><br></div><div>Sincerely,</div><div>Sapna</div><div><br></div></blockquote><br><blockquote type="cite"><div><div>nstxout = 0000 ; write coords</div></div></blockquote><div><br></div>What that mean? You better give a number bigger than 0.</div><div><br><blockquote type="cite"><div><div>gen_seed = 372340 ; random seed</div></div></blockquote><div><br></div>Just a remark, you can use -1 here for a random number base on time and process number.</div><div><br></div><div><blockquote type="cite"><div>
<div>constraint_algorithm = shake</div></div></blockquote><div><br></div>Any reason why not to using LINCS?</div><div><br></div><br><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: -webkit-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; ">-----<br>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br><br>===========================================<br>| Itamar Kass, Ph.D.<br>| Postdoctoral Research Fellow<br>|<br>| Department of Biochemistry and Molecular Biology<br>| Building 77 Clayton Campus<br>| Wellington Road<br>| Monash University,<br>| Victoria 3800<br>| Australia<br>|<br>| Tel: +61 3 9902 9376<br>| Fax: +61 3 9902 9500<br>| E-mail: <a href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>============================================<br></span>
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