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<TD>Hello,<br >Thankyou Drs Mark Abraham and Caterina Arcangeli for the useful suggestions. They worked for me. I could cat the two trr files and calculate the backbone g_rms values. I have to yet see how much they deviate with the original structures. I have couple of questions:<br ><br >If I do the MD studies using Gromacs 3.1 and Gromacs 3.3 with differennt forcefields like ffg43a1 and ffG53a5 respectively in the same simulating conditions how different would be my results ? or will there be any difference ?<br ><br >Is there a difference in the speed of the simulations say if I run them on SGI Octane R12000 and a Personal computer with 512 RAM Pentium III ? Incidently Gromacs 3.1 is loaded on Octane and Gromacs 3.3 on Pentium III .<br ><br >Why I am asking the second question is that the time taken on Octane is much larger ( around 9 days) compared to the Pentium III (3 days) what may be the reason ? <br ><br >Thanks for the patience ...<br ><br >regards<br >A .Sharada Devi<br >Technical Officer C<br >Center for Cellular Molecular <br >Biology<br >Habsiguda Uppal Road<br >Hyderabad -500007<br >India <br ><strong><em><br >-- Original Message --</em></strong><br >From: Caterina Arcangeli <caterina.arcangeli@casaccia.enea.it><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Wed, 03 Jan 2007 10:11:45 +0100<br >Subject: Re: [gmx-users] (no subject)<br ><br ><br >Hi,<br >using the command:<br >trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -o nchnp3_15pep.trr -settime<br ><br >the program will ask you the start time of each file. Try putting "5001"<br >for the first file and "c" (continue) for the second file.<br >It should be work.<br ><br >Ciao<br >Caterina<br ><br ><br ><br >Mark Abraham wrote:<br >> sharada wrote:<br >>> Hello gmx_users,<br >>><br >>> I wish you a very happy and prosperous new year 2007. I have a very<br >>> fundamental question in trjcat usage. I have two *.trr files of 5ns<br >>> and 10 ns runs . I would like to concanate the two and make a 15ns<br >>> trr file. How to give the command so that the starting time of the<br >>> 10ns file should be 5001ps and not 0ps and end time is 15000ps and not<br >>> 10000 ps. May this is a trivial question. Kindly help. I have tried<br >>> using the following command :<br >>> trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -settime -o<br >>> nchnp3_15pep.trr -b 0.00 -e 15000<br >> <br >> It's just like the command line utility cat... it will do a straight<br >> concatenation.<br >> <br >> trjcat -f 5n.trr 10n.trr -o 15n.trr<br >> <br >> should do what you want.<br >> <br >> Check using gmxdump , of course<br >> <br >> Mark<br >> _______________________________________________<br >> gmx-users mailing list gmx-users@gromacs.org<br >> http://www.gromacs.org/mailman/listinfo/gmx-users<br >> Please don't post (un)subscribe requests to the list. Use the www<br >> interface or send it to gmx-users-request@gromacs.org.<br >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br >> <br ><br ><br >-- <br >Caterina Arcangeli<br >ENEA, Computing and Modelling Unit (CAMO)<br >Casaccia Research Center - Post Bag 026<br >Via Anguillarese 301 - 00060 Roma<br >phone +39 06.3048.6898<br >fax +39 06.3048.6860<br >http://www.enea.it<br >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to gmx-users-request@gromacs.org.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br ></TD>
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