Re: [gmx-users] gromacs versus amber boxsize -correction-
Hi, On Tuesday, 29. January 2008 13:14, servaas michielssens wrote: > I made a mistake in the numbers, but the question remains: > > I ran the following command in gromacs: > editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 With -d and a triclinic box the size of the system in the x, y and z directions is used. With -d and cubic, dodecahedron or octahedron boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance. [from editconf -h] > > The equivalent command in amber: > solvateoct p61_vac.pdb TIP3PBOX 8.0 generates a truncated octahedron periodic box > > As far as I understand this, both command created a box were the edges are > 0.8 nm away from the solute. But the resulting image distance (d in the > manual) in gromacs is: 121.3092 > and in amber: > 110.5103716 > > This is makes a hugde difference in the number of water atoms to add. > Does anyone has an explanation for this paradox? so you generate two different boxsizes or types. > > > kind regards, > > servaas greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] gromacs versus amber boxsize
On Tue, 29 Jan 2008 12:57:13 +0100 "servaas michielssens" <[EMAIL PROTECTED]> wrote: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is: 121.3092 and in amber: 85.9385483 the box size is changing that fast? Which one is the right value? This is makes a hugde difference in the number of water atoms to add. Does anyone has an explanation for this paradox? kind regards, servaas - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] gromacs versus amber boxsize -correction-
On Tue, 29 Jan 2008 13:14:21 +0100 "servaas michielssens" <[EMAIL PROTECTED]> wrote: I made a mistake in the numbers, but the question remains: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 is there any reorientation in volved? As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) amber or gromacs manual? in gromacs is: 121.3092 and in amber: 110.5103716 Are the d the same in both programs? The definitions of dodecahedron are different in gromacs and gromos. could be a similar problem in with amber! Note however that the gromacs definition decreased the volume as compared to gromos. This is makes a hugde difference in the number of water atoms to add. Does anyone has an explanation for this paradox? kind regards, servaas - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] gromacs versus amber boxsize -correction-
servaas michielssens wrote: I made a mistake in the numbers, but the question remains: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is: 121.3092 and in amber: 110.5103716 What shapes were these commands creating? How are you measuring this image distance? Mark ___ gmx-users mailing listgmx-users@gromacs.org 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] gromacs versus amber boxsize
I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is: 121.3092 and in amber: 85.9385483 This is makes a hugde difference in the number of water atoms to add. Does anyone has an explanation for this paradox? kind regards, servaas___ gmx-users mailing listgmx-users@gromacs.org 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] gromacs versus amber boxsize -correction-
I made a mistake in the numbers, but the question remains: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is: 121.3092 and in amber: 110.5103716 This is makes a hugde difference in the number of water atoms to add. Does anyone has an explanation for this paradox? kind regards, servaas___ gmx-users mailing listgmx-users@gromacs.org 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
