Hi Mark<br>I read the manual and I used umabrella sampling and I got a curve for pmf but now I want to calculate pmf by energy perturbation that I want to sure about my curve that I got by umbrella sampling.<br>my question is about .itp file and how do I create.<br>thank you very much.<br><br><b><i>gmx-users-bounces@gromacs.org</i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> The results of your email command are provided below. Attached is your<br>original message.<br><br>- Results:<br> Ignoring non-text/plain MIME parts<br><br>- Unprocessed:<br> I read the manual and I used umabrella sampling and I got a curve for pmf=<br> but now I want pmf by energy perturbation that I want to sure about my c=<br> urve that I got by umbrella sampling.<br> my question is about .itp file and how do I create.<br> thank you very much.<br> Mark Abraham <mark.abraham@anu.edu.au> wrote:
><br> > Hi Dear<br> > I want to copute PMF between two amines by energy perturbation in<br> > gromacs<br> > but I do'nt know what do I?<br> > I read the manual and mailing list but I cann't solve it. if you are<br> > having<br> > informatin please help me?<br> You've been asking this question for months it seems, and you're not<br> getting a substantive answer because it is too general. If you've read th=<br> e<br> manual, then you will have been able to choose one of several types of PM=<br> F<br> calculation implemented in GROMACS to do, and then to make further<br> choices. Nobody is going to make these decisions for you. Maybe we'd<br> provide advice if you laid out the pros and cons for the choices and we<br> had suitable expertise.<br><br>- Ignored:<br> <br> For advice on asking questions the smart way so as to get useful answers,<br> check out
http://www.catb.org/~esr/faqs/smart-questions.html. In short,<br> from that article, the more you're seen to be working toward your own<br> solution, the more people are likely to want and be able to help you.<br> <br> Mark<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> !<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> =20<br> ---------------------------------<br> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try i=<br> t now.<br><br>- Done.<br><br>Date: Tue, 8 Jan 2008 22:25:31 -0800 (PST)<br>From: Farzad Molani
<farzad_c81@yahoo.com><br>Subject: Re: [gmx-users] energy perturbation<br>To: gmx-users-request@gromacs.org<br><br> Hi Mark<br>I read the manual and I used umabrella sampling and I got a curve for pmf but now I want pmf by energy perturbation that I want to sure about my curve that I got by umbrella sampling.<br>my question is about .itp file and how do I create.<br>thank you very much.<br><br><b><i>Mark Abraham <mark.abraham@anu.edu.au></i></b> wrote:</mark.abraham@anu.edu.au><blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> ><br>> Hi Dear<br>> I want to copute PMF between two amines by energy perturbation in<br>> gromacs<br>> but I do'nt know what do I?<br>> I read the manual and mailing list but I cann't solve it. if you are<br>> having<br>> informatin please help me?<br><br>You've been asking this question for months it seems, and you're not<br>getting a substantive
answer because it is too general. If you've read the<br>manual, then you will have been able to choose one of several types of PMF<br>calculation implemented in GROMACS to do, and then to make further<br>choices. Nobody is going to make these decisions for you. Maybe we'd<br>provide advice if you laid out the pros and cons for the choices and we<br>had suitable expertise.<br><br>For advice on asking questions the smart way so as to get useful answers,<br>check out http://www.catb.org/~esr/faqs/smart-questions.html. In short,<br>from that article, the more you're seen to be working toward your own<br>solution, the more people are likely to want and be able to help you.<br><br>Mark<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></blockquote><br><div> </div><hr size="1">Be a better friend, newshound, and know-it-all with Yahoo! Mobile. <a href="http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ%20"> Try it now.</a></blockquote><br><p> 
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