<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><p class="MsoNormal"><span class="apple-style-span"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;color:black">Ok, thanks for the comments! I
think I will conduct the simulation with </span>‘</span><span class="apple-style-span"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
font-family:Arial;color:black">constraints=</span>hbonds</span><span class="apple-style-span"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
color:black">’, since I had done so in NAMD. I guess it wouldn't bring big
problem to the trajectory except increasing the compute cost.</span></span><span lang="EN-US" style="font-size:12.0pt;mso-font-kerning:0pt"><o:p></o:p></span></p><br><br><div id="addMailSign"><span> </span></div><div id="mailcontent"><blockquote dir="ltr" style="border-left:2px solid #000000;margin-left:10px;margin-right:0px;padding-left:5px;padding-right:0px;font-family:宋体;font-style:normal;font-variant:normal;font-weight:normal;font-size: 9pt;line-height:normal;font-size-adjust:none;font-stretch:normal;"><p><br></p><div class="sohu_quote" style="">----- Original Message -----<br>From: xhomes@sohu.com<br>Date: Wednesday, June 2, 2010 14:17<br>Subject: Re: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option.<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br><br><p><span style="font-size: 12pt;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi, Mark,</span></p><p></p><p></p> <p><span style="font-size: 12pt;"><span style=""><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </span></span></p><p></p><p></p> <p><span style="font-size: 12pt;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I’ve noticed about the minimum cell diameter restrict, but I still had no idea about how to adjust the related parameter after I read the manual part mentioned by the error info. I don’t have too much understanding about the algorithm, so I turned around to rely on the ‘-pd’ option:)</span></p><p>OK, but my point is that if you know you need constraints=all-bonds, then you need a bigger system before GROMACS will be able to parallelise it.<br><span style="font-size: 12pt;"></span></p><p></p><p></p> <p><span style="font-size: 12pt;"><span style=""><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </span></span></p><p></p><p></p> <p><span style="font-size: 12pt;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>About choosing double precision, I notice </span><span style="font-size: 11pt; font-family: NimbusRomNo9L-Regu;">normal mode analysis need the dou</span><span style="font-size: 12pt;">ble precision version of some programs. And I don’t know whether I should use double precision version of mdrun for covariance analysis, so I just chose the double one! <br></span></p><p>Sure, doing EM in double is standard advice for preparing for NMA.<br><span style="font-size: 12pt;"></span></p><p></p><p></p> <p><span style="font-size: 12pt;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I also don’t have too much idea about choosing which ensemble to conduct covariance analysis. I’ve noticed that temperature coupling would ‘correct’ the motion of the atoms. I think a more ‘natural’ trajectory with least artifact should be generated for covariance analysis. Any comments about this?</span></p><p></p><p></p>One "always" wants accurate thermodynamic sampling of the target ensemble. What ensemble to target depends mostly on your simulation objective. NPT usually makes the most sense for comparision with experimental data. You should read up on the algorithms that regulate T and P to see what the wisest choices may be with respect to accurate sampling, because there are sound reasons for one choice or another. Start with the GROMACS manual.<br><br>Mark<br>-- <br></div><p></p></blockquote></div>