Re: [gmx-users] Re: shake vs settle for water
Rahul Godawat wrote: Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time step 2 fs.. and OS --- RedHat Enterprise Linux, I hv been using 3.2.1 for a while apart from that no specific reason for using 3.2.1 dt = 0.002; time step (ps) nsteps = 10 ; number of steps comm_mode = Linear comm_grps = System energygrps = OW HW try removing the line above nstcomm = 10 ; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 500 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.0 ; cut-off for vdw rcoulomb= 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t = 0.5 ref_t = 300 Thanks -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, June 07, 2006 3:35 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 26, Issue 32 Send gmx-users mailing list submissions to gmx-users@gromacs.org 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. Free volume: Pass and Gromacs (Alessandro Mattozzi) 2. Re: Free volume: Pass and Gromacs (David van der Spoel) 3. Re: Freezing part of the molecules!!! (Soren Enemark) 4. Re: Freezing part of the molecules!!! (David van der Spoel) 5. shake vs settle for water (Rahul Godawat) 6. diffusivity computations (Debashis Dutta) 7. Re: shake vs settle for water (David van der Spoel) -- Message: 1 Date: Wed, 7 Jun 2006 17:11:03 +0200 From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> Subject: [gmx-users] Free volume: Pass and Gromacs To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? -Segmentation fault Suggestion: I use trjconv to get a pdb; is it possible that I am doing some mistake in the conversion? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060607/ace7fa15/att achment-0001.html -- Message: 2 Date: Wed, 07 Jun 2006 17:14:59 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Free volume: Pass and Gromacs To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Alessandro Mattozzi wrote: Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? Yes. make an index file, it will have a suitable group for it. -Segmentation fault Suggestion: I use trjconv to get a pdb; is it possible that I am doing some mistake in the conversion? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTE
[gmx-users] Re: shake vs settle for water
Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time step 2 fs.. and OS --- RedHat Enterprise Linux, I hv been using 3.2.1 for a while apart from that no specific reason for using 3.2.1 dt = 0.002; time step (ps) nsteps = 10 ; number of steps comm_mode = Linear comm_grps = System energygrps = OW HW nstcomm = 10 ; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 500 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.0 ; cut-off for vdw rcoulomb= 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t = 0.5 ref_t = 300 Thanks -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, June 07, 2006 3:35 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 26, Issue 32 Send gmx-users mailing list submissions to gmx-users@gromacs.org 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. Free volume: Pass and Gromacs (Alessandro Mattozzi) 2. Re: Free volume: Pass and Gromacs (David van der Spoel) 3. Re: Freezing part of the molecules!!! (Soren Enemark) 4. Re: Freezing part of the molecules!!! (David van der Spoel) 5. shake vs settle for water (Rahul Godawat) 6. diffusivity computations (Debashis Dutta) 7. Re: shake vs settle for water (David van der Spoel) -- Message: 1 Date: Wed, 7 Jun 2006 17:11:03 +0200 From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> Subject: [gmx-users] Free volume: Pass and Gromacs To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? -Segmentation fault Suggestion: I use trjconv to get a pdb; is it possible that I am doing some mistake in the conversion? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060607/ace7fa15/att achment-0001.html -- Message: 2 Date: Wed, 07 Jun 2006 17:14:59 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Free volume: Pass and Gromacs To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Alessandro Mattozzi wrote: > Hi all > I wonder if anybody has been using Pass to measure free volume: I got > these errors: > > -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. > Suggestion: Do I have to remove all the dummies? Yes. make an index file, it will have a suitable group for it. > > -Segmentation fault > Suggestion: I use trjconv to get a pdb; is it possible that I am doing > some mistake in the conversion? > > Thanx > > Alessandro Mattozzi > M.Phil., Ph.D. student > Dept. of Fibre and Polymer Technology > Royal Institute of Technology > Stockholm, Sweden > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROT
[gmx-users] Re: shake vs settle for water
Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time step 2 fs.. dt = 0.002; time step (ps) nsteps = 10 ; number of steps comm_mode = Linear comm_grps = System energygrps = OW HW nstcomm = 10 ; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 500 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.0 ; cut-off for vdw rcoulomb= 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t = 0.5 ref_t = 300 Thanks -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, June 07, 2006 3:35 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 26, Issue 32 Send gmx-users mailing list submissions to gmx-users@gromacs.org 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. Free volume: Pass and Gromacs (Alessandro Mattozzi) 2. Re: Free volume: Pass and Gromacs (David van der Spoel) 3. Re: Freezing part of the molecules!!! (Soren Enemark) 4. Re: Freezing part of the molecules!!! (David van der Spoel) 5. shake vs settle for water (Rahul Godawat) 6. diffusivity computations (Debashis Dutta) 7. Re: shake vs settle for water (David van der Spoel) -- Message: 1 Date: Wed, 7 Jun 2006 17:11:03 +0200 From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> Subject: [gmx-users] Free volume: Pass and Gromacs To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? -Segmentation fault Suggestion: I use trjconv to get a pdb; is it possible that I am doing some mistake in the conversion? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060607/ace7fa15/att achment-0001.html -- Message: 2 Date: Wed, 07 Jun 2006 17:14:59 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Free volume: Pass and Gromacs To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Alessandro Mattozzi wrote: > Hi all > I wonder if anybody has been using Pass to measure free volume: I got > these errors: > > -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. > Suggestion: Do I have to remove all the dummies? Yes. make an index file, it will have a suitable group for it. > > -Segmentation fault > Suggestion: I use trjconv to get a pdb; is it possible that I am doing > some mistake in the conversion? > > Thanx > > Alessandro Mattozzi > M.Phil., Ph.D. student > Dept. of Fibre and Polymer Technology > Royal Institute of Technology > Stockholm, Sweden > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
