<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Sapna,</div><div><br></div><div>It is a good question, but such of personal preferences. I found out that my simulations tend to crash more often when I am using 4.5.5. It might be the General-reaction -field I use or something else, I am not sure. Also, it seems I will not gain much from upgrading, so I stick to 4.0.7.</div><div><br></div><div>All this is not to say that 4.5.5 is not a good simulation package. It is a good and useful MD package, and I highly appreciate all the time and effort put into it.</div><div><br></div><div>Best,</div><div>Itamat</div><div><br></div><div>PS, there are still people around using 3.3.3 or even 3.2.1, so I am not that behind. </div><br><div><div>On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Itamar,<div><br></div><div>Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version?</div><div><br></div><div>Sapna<br>
<br><div class="gmail_quote">On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass <span dir="ltr"><<a href="mailto:itamar.kass@monash.edu">itamar.kass@monash.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word">Hi Sapna,<div><br></div><div>I had the same problem few weeks ago.</div><div><br></div><div>Apparently, some parameters are different (eg. nstpcouple).</div><div><br></div><div>Cheers,</div>
<div>Itamar<font color="#888888"><br></font><div><br></div><div>PS I found out that I prefer to stick to 4.0.7.</div><div><br></div><div><br></div><div></div></div></div><br><div style="word-wrap:break-word"><div><div><br>
<div><div>On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote:</div><br><blockquote type="cite"><font size="3">Dear All,</font>
<div><font size="3"><br></font></div><div><font size="3">I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated.</font></div>
<div><font size="3"><br></font></div><div><font size="3">MDP File </font></div><div><font size="3"><br></font></div><div><font size="3"><div>
title = 100% occupancy CO2 hydrate ; a string</div><div>cpp = /lib/cpp ; c-preprocessor</div><div>dt = 0.002 ; time step</div><div>nsteps = 15000000 ; number of steps</div>
<div>nstcomm = 10 ; reset c.o.m. motion</div><div>nstxout = 0000 ; write coords</div><div>nstvout = 0000 ; write velocities</div><div>
nstlog = 25000 ; print to logfile</div>
<div>nstenergy = 500 ; print energies</div><div>xtc_grps = OW_HW1_HW2_CO2 </div><div>nstxtcout = 1000</div><div>nstlist = 10 ; update pairlist</div>
<div>ns_type = grid ; pairlist method</div><div>coulombtype = PME</div><div>rvdw = 1.2 ; cut-off for vdw</div><div>rcoulomb = 1.2 ; cut-off for coulomb</div>
<div>rlist = 1.2 ; cut-off for coulomb</div><div>DispCorr = EnerPres</div><div>Tcoupl = Nose-Hoover</div><div>ref_t = 270 </div><div>tc-grps = System</div>
<div>tau_t = 0.5 </div><div>Pcoupl = Parrinello-Rahman</div><div>Pcoupltype = semiisotropic ; pressure geometry</div><div>tau_p = 1.0 1.0 ; p-coupoling time</div>
<div>compressibility = 4.5e-5 4.5e-5 ; compressibility</div><div>ref_p = 30.5 30.5 ; ref pressure</div><div>gen_vel = yes ; generate initial vel</div>
<div>gen_temp = 260 ; initial temperature</div><div>gen_seed = 372340 ; random seed</div><div>constraint_algorithm = shake</div><div>constraints = all-bonds </div>
<div><br></div></font></div><div><font size="3">-------</font></div><div><font size="3"><br></font></div><div><font size="3"><br></font></div><div>
<font size="3">Thank you,</font></div><div><font size="3"><br></font></div><div><font size="3">Sincerely,</font></div><div><font size="3">Sapna</font></div>
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-----<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: <a href="tel:%2B61%203%209902%209376" value="+61399029376" target="_blank">+61 3 9902 9376</a><br>
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<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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