Hi there, I would be glad if you let me know how can I use a pdb file with CSDs in GROMACS. Thank you very much. --- [EMAIL PROTECTED] wrote:
> Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, > visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body > 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it > is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. "Specified frame doesn't exist or file not > seekable" when > using .xtc (Qiao Baofu) > 2. Re: "Specified frame doesn't exist or file not > seekable" when > using .xtc (David van der Spoel) > 3. Re: "Specified frame doesn't exist or file not > seekable" when > using .xtc (Qiao Baofu) > 4. Re: "Specified frame doesn't exist or file not > seekable" when > using .xtc (David van der Spoel) > 5. *.gro output file being written to inverse > (Luciano Costa) > 6. mdrun 3.3.2 crash - gmx_sumi called in serial > run with RF > (Michel Cuendet) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Nov 2007 16:17:32 +0100 > From: "Qiao Baofu" <[EMAIL PROTECTED]> > Subject: [gmx-users] "Specified frame doesn't exist > or file not > seekable" when using .xtc > To: [email protected] > Message-ID: > > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, all > > When I using the .xtc file to analyse, I always meet > the following error > information > Specified frame doesn't exist or file not seekable > While it works when using the .trr file. In > analyzing, only the coordinate > is used. Therefore, I want to use .xtc file. In this > way, it runs a little > faster. However, the above proble exits. What's > wrong with the .xtc file? > and how to solve it? > > Thanks! > > -- > Sincerely yours, > Dr. Baofu Qiao > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20071101/dff744c6/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 01 Nov 2007 16:19:29 +0100 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] "Specified frame doesn't > exist or file not > seekable" when using .xtc > To: Discussion list for GROMACS users > <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > > Qiao Baofu wrote: > > Hi, all > > > > When I using the .xtc file to analyse, I always > meet the following error > > information > > Specified frame doesn't exist or file not > seekable > > While it works when using the .trr file. In > analyzing, only the > > coordinate is used. Therefore, I want to use .xtc > file. In this way, it > > runs a little faster. However, the above proble > exits. What's wrong > > with the .xtc file? and how to solve it? > > > gmx version please. > > Thanks! > > > > -- > > Sincerely yours, > > Dr. Baofu Qiao > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., > Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > > > ------------------------------ > > Message: 3 > Date: Thu, 1 Nov 2007 16:27:39 +0100 > From: "Qiao Baofu" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] "Specified frame doesn't > exist or file not > seekable" when using .xtc > To: "Discussion list for GROMACS users" > <[email protected]> > Message-ID: > > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am using Gromacs 3.3.1. The .xtc file is obtained > from mdrun, as shown in > the following > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) > and forces (f) > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Checkpointing helps you continue after crashes > nstcheckpoint = 0 > ; Output frequency for energies to log file and > energy file > nstlog = 1000 > nstenergy = 100 > ; Output frequency and precision for xtc file > nstxtcout = 10 > xtc-precision = 1000 > > > > > > 2007/11/1, David van der Spoel > <[EMAIL PROTECTED]>: > > > > Qiao Baofu wrote: > > > Hi, all > > > > > > When I using the .xtc file to analyse, I always > meet the following error > > > information > > > Specified frame doesn't exist or file not > seekable > > > While it works when using the .trr file. In > analyzing, only the > > > coordinate is used. Therefore, I want to use > .xtc file. In this way, it > > > runs a little faster. However, the above proble > exits. What's wrong > > > with the .xtc file? and how to solve it? > > > > === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ 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
