Dear Prof. Spoel, <br> <br> Many thanks for your reply.<br> <br> Since the fourier_n* values are associated with the grid sizing, will these values affect my results drastically? do you suggest resubmitting these runs?<br> <br> regards,<br> Pri...<br> <br><br><b><i>David van der Spoel <spoel@xray.bmc.uu.se></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> priyanka srivastava wrote:<br>> Hie,<br>> <br>> Many thanks for your reply.<br>> <br>> Yes I have used semi-isotropic coupling.<br>> <br>> Another doubt is why only a value of 4.5e-5?<br>> <br>> I have used PME and have mentioned rcoulomb in the<br>> .mdp file too, which as is pointed out by you, has no<br>> meaning!! But does this mean that my mdp file is<br>> wrong? Because if PME does not use rcoulomb it shud<br>> simply ignore the value.<br>> Actually I do not want to use twin range
cutoff. So, I<br>> have given rvdw = rlist. Is this alright?<br>> Portion of my mdp file looks like this:<br>> <br>> ; Electrostatics<br>> coulombtype = PME<br>> fourier_nx = 6.4<br>> fourier_ny = 5.0<br>> fourier_nz = 8.1<br>these numbers should be integers<br><br><br>> pme_order = 4<br>> rcoulomb = 1.5<br>> rvdw = 1.5<br>> <br>> Also since I have not specified "vdwtype" in the mdp<br>> file, so it automatically takes Cut-off.<br>> <br>> regards,<br>> Pri...<br>> <br>> <br>> --- Martin H�fling <martin.hoefling @gmx.de=""> wrote:<br>> <br>>> Am Mittwoch, 20. Juni 2007 schrieb priyanka<br>>> srivastava:<br>>><br>>>> I am currently involved in doing a lipid-peptide<br>>>> simulation under NPAT conditions. The way I have<br>>>> applied NPAT condition is as
follows:<br>>>><br>>>> ref_p = 0 1<br>>>> compressibility = 0.0 4.5e-5<br>>> with semiisotropic?<br>>><br>>>> Although while performing analysis it shows that<br>>> the x<br>>>> and y dimensions are constant but still I am not<br>>> sure<br>>>> about the way I have applied NPAT. Could somone<br>>> please<br>>>> tell me the basis behind it?<br>>> If i am remembering correctly, this is what above<br>>> values should do:<br>>><br>>> first dimension is x-y second one is the z<br>>> direction. Reference pressure is 1 <br>>> for both (obviously makes sense) whereas<br>>> compressibility set to 0 for x-y <br>>> plane prevents box changes in x and y direction. So<br>>> only z-direction remains <br>>> for adjusting pressure.<br>>><br>>>> Another thing is I have used vdwtype:
cutoff.<br>>>> But my intention is not to use the twin range<br>>> cutoff<br>>>> at all!! In my case rlist = rcoulomb = rvdw, i.e.<br>>> all<br>>>> three are same!! Is this alright? (the coulombtype<br>>>> = PME)<br>>> Sorry, didn't get that part of your question. Can<br>>> you post relevant parts of <br>>> your mdp and specify it further? Chapter 7 says that<br>>> parameters for PME are <br>>> fourierspacing and pme_order, rcoulomb should not be<br>>> used then.<br>>><br>>> Cheers<br>>> Martin<br>>> _______________________________________________<br>>> gmx-users mailing list gmx-users@gromacs.org<br>>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>>> Please search the archive at<br>>> http://www.gromacs.org/search before posting!<br>>> Please don't post (un)subscribe requests to the<br>>> list. Use the
<br>>> www interface or send it to<br>>> gmx-users-request@gromacs.org.<br>>> Can't post? Read<br>>> http://www.gromacs.org/mailing_lists/users.php<br>>><br>> <br>> <br>> <br>> <br>> ____________________________________________________________________________________<br>> Pinpoint customers who are looking for what you sell. <br>> http://searchmarketing.yahoo.com/<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<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><br><br>--
<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<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></martin.hoefling></blockquote><br><p> 
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