Dear gmx-users, I'm trying to perform some REMD calculations with GROMACS 4.0.5, and I found on the Wiki site these instructions:
http://oldwiki.gromacs.org/index.php/REMD that I'm trying to follow, but I encountered some problems. If I understand well the instructions, if I want to perform replicas at N different temperatures, I have to create N different .mdp files and then N different .tpr files, that I should name "filename"_0, "filename"_1... "filename"_N-1. That's what I did: I created 16 different .mdp files and 16 .tpr files that I called REMD_0.tpr. REMD_1.tpr REMD_2.tpr ... REMD_15.tpr. At this point, I have to launch the mdrun command with the -multi, -replex (optionally, -reseed) options. Following the example in "Execution step", my command line should be: mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_ -np 16 That's what I did, but I experienced some difficulties on the parallel machines that I'm using to perform simulations. In particular, I inserted the above command into a script that is used on the machine to launch the program in an interactive way, but GROMACS returns an error saying that "cannot open file REMD_.tpr" (and in fact, the file REMD_.tpr does not exist, only files REMD_0.tpr, REMD_1.tpr etc do exist!) I also retried launching the same command from the shell, but the error was the same. So my question is: how does GROMACS "understand" that it has to interpret "REMD_.tpr" not as a single file, but as a group of files indexed _0, _1, _2 and so on? Does it depend on the order of the options? Could you please give me some hints about? BTW, another problem: I tried to find solution searching in the oldwww.gromacs.org site, but I am still unable to consult the gmx-users archives using a keyword as it was possible in the past. How can I find information in the GROMACS archives? Many thanks and regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: [email protected] Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito"
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