[gmx-users] last line in .gro file
Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? Thanks, vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Dear Justin, I am trying to set up calculations for a cellulose structure. The allomorph of cellulose which I want to study has a monoclinic structure. I have a .cif file of the XRD structure. I think the better question to ask is how can I make input files using that. thanks vishal On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Vishal Agarwal wrote: Dear Justin, I am trying to set up calculations for a cellulose structure. The allomorph of cellulose which I want to study has a monoclinic structure. I have a .cif file of the XRD structure. I think the better question to ask is how can I make input files using that. That is a far more complex question. There are numerous posts in the list archive regarding preparing input for polymeric systems, so please do search the list archive. I helped one user set up a polyethylene system some time ago, so that may help out. You'll have to familiarize yourself with .rtp entry construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to work though. There are lots of resources in the manual and on the Gromacs wiki pages to get you started. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards
Re: [gmx-users] last line in .gro file
Dear Justin, Thanks for replying. You mentioned that gromacs supports triclinic structure. Can you tell me what will be the box parameters for triclinic structure of cell parameters a, b, c and angles alpha, beta and gama. Thanks in advance Vishal On Tue, Feb 2, 2010 at 12:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, I am trying to set up calculations for a cellulose structure. The allomorph of cellulose which I want to study has a monoclinic structure. I have a .cif file of the XRD structure. I think the better question to ask is how can I make input files using that. That is a far more complex question. There are numerous posts in the list archive regarding preparing input for polymeric systems, so please do search the list archive. I helped one user set up a polyethylene system some time ago, so that may help out. You'll have to familiarize yourself with .rtp entry construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to work though. There are lots of resources in the manual and on the Gromacs wiki pages to get you started. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. Are you talking about your unit cell type, or the structure of the species you wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is it listed as a type of box that can be defined with editconf, so you need to clarify what it is you're trying to do. In any case, the last line of the .gro file corresponds to the box vectors of the unit cell you specify with editconf. If you don't specify anything explicitly, the default is to build a triclinic unit cell. -Justin thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] last line in .gro file
Hi, Since any unit cell can be formulated as a triclinic cell, the monoclinic cell is indeed supported. By definition it has two 90 degree angles and one that is not 90 degrees. The box vectors can be of different lengths. You'll have to do the math and reading yourself to find out how this translates to a .gro box. The manual is your friend here. Good luck, Erik Vishal Agarwal skrev: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Hi Vishal, Here is a python function that generates a triclinic representation given a definition with lengths and angles. The argument L is a tuple or list containing the lengths and angles. def triclinic(L): B = [[0,0,0],[0,0,0],[0,0,0]] x, y, z, a, b, c = L[:6] B[0][0] = x if a == 90 and b == 90 and c == 90: B[1][1] = y B[2][2] = z else: a = a*pi/180 b = b*pi/180 c = c*pi/180 B[1][0] = y*cos(c) B[1][1] = y*sin(c) B[2][0] = z*cos(b) B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c) B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2) return B Hope it helps, Tsjerk On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Since any unit cell can be formulated as a triclinic cell, the monoclinic cell is indeed supported. By definition it has two 90 degree angles and one that is not 90 degrees. The box vectors can be of different lengths. You'll have to do the math and reading yourself to find out how this translates to a .gro box. The manual is your friend here. Good luck, Erik Vishal Agarwal skrev: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] last line in .gro file
Hi Tsjerk, Thanks for replying. I was going through the pdb format dcoument on the PDB webpage. I found that the box corresponds to the following: a b(cos(gama)) c(cos(beta)) 0 b(sin(gama)) c(cos(alpha) - cos(beta) cos(gama) / sin(gama) 00 V/(ab sin(gama)) where V = abc(1 - (cos(alpha))^2 - (cos(beta))^2 - (cos(gama))^2+ 2cos(alpha) cos(beta) cos(gama))^1/2 This corresponds to general form in representing these vectors. The following code also desolves to this form. Thank you again. Best, Vishal P.S. I thank all who have replied to this mail. On Tue, Feb 2, 2010 at 3:44 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vishal, Here is a python function that generates a triclinic representation given a definition with lengths and angles. The argument L is a tuple or list containing the lengths and angles. def triclinic(L): B = [[0,0,0],[0,0,0],[0,0,0]] x, y, z, a, b, c = L[:6] B[0][0] = x if a == 90 and b == 90 and c == 90: B[1][1] = y B[2][2] = z else: a = a*pi/180 b = b*pi/180 c = c*pi/180 B[1][0] = y*cos(c) B[1][1] = y*sin(c) B[2][0] = z*cos(b) B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c) B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2) return B Hope it helps, Tsjerk On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Since any unit cell can be formulated as a triclinic cell, the monoclinic cell is indeed supported. By definition it has two 90 degree angles and one that is not 90 degrees. The box vectors can be of different lengths. You'll have to do the math and reading yourself to find out how this translates to a .gro box. The manual is your friend here. Good luck, Erik Vishal Agarwal skrev: Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Vishal Agarwal wrote: Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y] Can anyone explain what each of these mean in terms of cell parameters ? The last line contains the box vectors. Specifics in terms of unit cell geometry are given in the manual, Table 3.1 and section 3.2.1. -Justin Thanks, vishal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards *** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *** 'Your only obligation in any lifetime is to be true to yourself. ---Richard Bach -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
