Re: [gmx-users] a box of water
On 9/7/12 7:34 AM, Turgay Cakmak wrote: Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I did geometry optimization for nsteps= 5. Now, can I continue with production run or do I need to do equilibration runs to arrive correct temperature and pressure? Equilibration is always advisable, though for a system of water you don't do any sort of position-restrained steps as you would if there were a solute. In any case, if you do not run explicit NVT and/or NPT phases, you'll have to throw out some of the beginning of the production trajectory anyway, since generation of velocities does not guarantee that you maintain any sort of equilibrated state, so the beginning of the run is equilibration. For stability reasons, NVT and NPT are advisable. Water is pretty robust, but why take a chance when equilibration steps are fast to do? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] a box of water
Thanks a lot for your quick reply Justin. I got it. Turgay 2012/9/7 Justin Lemkul jalem...@vt.edu: On 9/7/12 7:34 AM, Turgay Cakmak wrote: Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I did geometry optimization for nsteps= 5. Now, can I continue with production run or do I need to do equilibration runs to arrive correct temperature and pressure? Equilibration is always advisable, though for a system of water you don't do any sort of position-restrained steps as you would if there were a solute. In any case, if you do not run explicit NVT and/or NPT phases, you'll have to throw out some of the beginning of the production trajectory anyway, since generation of velocities does not guarantee that you maintain any sort of equilibrated state, so the beginning of the run is equilibration. For stability reasons, NVT and NPT are advisable. Water is pretty robust, but why take a chance when equilibration steps are fast to do? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] velacc box of water
Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 ___ 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] velacc box of water
Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.eduwrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 ___ 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] velacc box of water
Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] velacc box of water
Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.commailto: jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] velacc box of water
Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this actually worked. and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to Very weird. Both of your commands worked on my machine. What version of Gromacs are you using? Does genbox work for other systems? -Justin create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] velacc box of water
I converted spc216.pdb to gro using editconf. SO they must be the same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine? On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this actually worked. and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to Very weird. Both of your commands worked on my machine. What version of Gromacs are you using? Does genbox work for other systems? -Justin create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie
Re: [gmx-users] velacc box of water
Jamie Seyed wrote: I converted spc216.pdb to gro using editconf. SO they must be the I suppose that's fine, I just don't see all the need for interconverting file formats. It just opens up the possibility of more errors if you don't keep track of what you're doing :) same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine? I have the same version. The commands you showed completed in just a fraction of a second, like most simple solvation procedures. -Justin On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this actually worked. and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to Very weird. Both of your commands worked on my machine. What version of Gromacs are you using? Does genbox work for other systems? -Justin create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage
Re: [gmx-users] velacc box of water
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea? On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: I converted spc216.pdb to gro using editconf. SO they must be the I suppose that's fine, I just don't see all the need for interconverting file formats. It just opens up the possibility of more errors if you don't keep track of what you're doing :) same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine? I have the same version. The commands you showed completed in just a fraction of a second, like most simple solvation procedures. -Justin On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this actually worked. and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to Very weird. Both of your commands worked on my machine. What version of Gromacs are you using? Does genbox work for other systems? -Justin create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 Would you please inform me what are these number and what is the relation between them? Many Thanks in Advance/Jamie On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need
Re: [gmx-users] velacc box of water
Jamie Seyed wrote: Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea? Oops, I hadn't seen that before. That is what you should do. The -cp flag is the coordinate file that should have solvent added to it, and that's what you're after, isn't it? -Justin On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: I converted spc216.pdb to gro using editconf. SO they must be the I suppose that's fine, I just don't see all the need for interconverting file formats. It just opens up the possibility of more errors if you don't keep track of what you're doing :) same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine? I have the same version. The commands you showed completed in just a fraction of a second, like most simple solvation procedures. -Justin On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this actually worked. and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to Very weird. Both of your commands worked on my machine. What version of Gromacs are you using? Does genbox work for other systems? -Justin create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top or when I use this command: genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top It goes until Reading solvent configuration Solvent configuration contains 648 atoms in 216 residues and then stops Would you please let me know why it happens?? Many Thanks in Advance/Jamie Is resize.gro a new file? Or something you have created before (i.e., an empty file with a box size defined)? Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too small to contain 500 solvent molecules. Define an appropriate box size. -Justin On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks to Justin Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if
Re: [gmx-users] velacc box of water
Jamie Seyed wrote: Hi Justin, But this seems that did not change the number of molecule in the output (only the volume and density are changing) and it seems that -maxsol has not been used... my full command genbox -cp spc216.gro -maxsol 500 -o out.gro -p topol.top -box 4 4 4 if I change 500 to any thing else the result is the same and changing 4 4 4 to any thing else will change the volume and density... When simultaneously specifying -maxsol and -box, the two must work in harmony. A smaller box may not fit 500 molecules, and trying a larger number of molecules may not fit in a fixed 4x4x4 nm box. The command I used that worked was: genbox -cs spc216.gro -maxsol 500 -o out.gro -box 5 5 5 Note that this gives a weird output configuration, probably because the box is not appropriate, but at least its a template of a command that should, in theory, work. Alternatively, you can use the editconf/genbox combination to define a box and center the solute (which is water) with editconf -c, then fill the box with genbox, where -cp indeed specifies the solute (water) and provides solvent (water again!) with -cs. -Justin I got confused... I appreciate any hint on that/Thanks/Jamie On Sun, Oct 11, 2009 at 2:07 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Thanks Justin, As I understood -cp is for solute and -cs is for solvent... in this case I thought that small created volume of water are plying as solute... and then genbox should fill the box... Anyways thank you :-) On Sun, Oct 11, 2009 at 2:01 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea? Oops, I hadn't seen that before. That is what you should do. The -cp flag is the coordinate file that should have solvent added to it, and that's what you're after, isn't it? -Justin On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: I converted spc216.pdb to gro using editconf. SO they must be the I suppose that's fine, I just don't see all the need for interconverting file formats. It just opens up the possibility of more errors if you don't keep track of what you're doing :) same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine? I have the same version. The commands you showed completed in just a fraction of a second, like most simple solvation procedures. -Justin On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was editconf -bt cubic -f spc216.pdb -o resize.gro -d 1 Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this actually worked. and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you Mark suggested me to Very weird. Both of your commands worked on my machine. What version of Gromacs are you using? Does genbox work for other systems? -Justin create a box of water.../Many Thanks/Jamie On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu
Re: [gmx-users] velacc box of water
Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie genconf will allow you to stack multiples of that 216 box. Or, use editconf to adjust the size of a 216 box, and genbox to fill it to get a number that suits your fancy. In either case you will need to equilibrate before trying to measure velacc, just as with any other observable. Mark ___ 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] velacc box of water
Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
