<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Dear Gromacs users</span></div><div><span>I have checked something today and it seems starnge to me. Doing the Justin lyzozyme tutorial, I checked the performance of our parallel system. Subimitting the job on 8 processors of one node, I get<span style="color: rgb(255, 0, 255);"> </span><span style="text-decoration: underline; font-weight: bold; background-color: rgb(255, 255, 255); color: rgb(255, 0, 255);">0.86 ns/day</span><span style="color: rgb(255, 0, 255);"> </span>which seems to be very weak performance. Do you have any idea about the ns/day performance of 8 processors for the same lyzozyme system?</span></div><div><br><span></span></div><div><span>Thanks</span></div><div><span>Regards</span></div><div><span>D.M</span></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div
style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, 3 June 2012, 17:16<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Atomtype 1<br> </font> </div> <br><br><br>On 6/3/12 8:24 AM, xi zhao wrote:<br>> Dear gmx-users:<br>> I add a new residue in *rtp ,according to<br>> <a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>,<br>> and modified corresponding files :such as atp, hdb , after making a full copy of<br>> the
installed forcefield in woring diectory.<br>> When pdb2gmx_d<br>> appeared "<br>> All occupancies are one<br>> Opening force field file ./amber99sbr.ff/atomtypes.atp<br>> Atomtype 1"<br>> Please give me suggestions<br><br>Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines?<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org"
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