Thanks guys. I guess I'll be running it again. I only deshuffled 3) to 4)
On 9/14/07, Yang Ye <[EMAIL PROTECTED]> wrote: > On 9/14/2007 5:35 PM, [EMAIL PROTECTED] wrote: > > Selon Yang Ye <[EMAIL PROTECTED]>: > > > > > >> Deshuffling shall be made before 2), 3) and 4). > >> > > > > Furthermore, be aware that if you use the 'sort' option, you'll also need to > > desort ... > > IIRC, there is a g_desort program that does all in one (it was published on > > the > > list some time ago), and should be avaialbe in next gromacs version. > > > > Stéphane > > > Instead, -shuffle and -sort will all disappear in the next version. I > encourage Frankie to benchmark the speed-up ratio, especially it is not > a membrane system. I know that people would not use -sort/shuffle so as > not to mess things up for some "little" lost in speed. That's just alright. > >> On 9/14/2007 11:36 AM, Frankie Montenegro wrote: > >> > >>> Hi guys, > >>> > >>> A stupid question: I got myself confused with this > >>> shuffling/deshuffling thing, which I > >>> shouldn't have been doing with protein in the first place. So this > >>> are my steps, done > >>> on the same 4 nodes, please tell me whether I was supposed to do any > >>> deshuffling > >>> of .trr and .gro files, and following which steps: > >>> 1)minimization, supplied output .gro to the next step > >>> 2)equilibration, supplied output .gro to the next step > >>> 3) NVT run, supplied output .gro and .trr to the next step > >>> 4) NPT run > >>> > >>> A simple YES or NO for each step will suffice. > >>> > >>> Thanks, > >>> Frankie > >>> _______________________________________________ > >>> gmx-users mailing list [email protected] > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>> Please search the archive at http://www.gromacs.org/search before posting! > >>> Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to [EMAIL PROTECTED] > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >>> > >>> > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
