[gmx-users] Issuing multiple commands simultaneously
I have a series of commands which I want to run a simulation. Is there a way I can issue them together at the start such that the second command is automatically executed after the first one finishes and so on without any manual input. Thanks in advance. -- 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] Re:Applying periodic boundary conditions in energy minimization
Hi, After applying energy minimization most of the atoms leave the box ( around 95%). I am using a composite system of polymer and clay. The composite box (5.8 nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm * 5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox. I am not using any solvent in the system. Could that create a problem? Or could the problem be that the box dimensions are too small? In that case should I increase the size of the composite box. Also, If I increase the size of the box how do I ensure that the density of the system does not chance. Thanks for your help. -- Message: 3 Date: Thu, 4 Apr 2013 14:05:31 +0800 (CST) From: song.yongshun song.yongs...@163.com Subject: Re:[gmx-users] Applying periodic boundary conditions in energy minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 48b65938.13820.13dd3a668a3.coremail.song.yongs...@163.com Content-Type: text/plain; charset=ISO-8859-1 Hi, Actually you have already applied pbc,and there seems nothing wrong. Some atoms are out of the box is common. If your box vector is correct,then Gromacs will run successfuly afterwards. At 2013-04-03 22:51:54,Abhinav Agrawal abhv.a...@gmail.com wrote: Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz I used the following commands: grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2 mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log Can you please tell me what I am doing wrong. Thanks in advance -- 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
[gmx-users] Re: Re: Re: Applying periodic boundary conditions in energy minimization
I have a clay pdb file http://s24.postimg.org/je3mvov9h/MMT.png and a polymer structure file: http://s24.postimg.org/ei003zv45/PLA.png I use the following commands to generate a composite box genbox -cp mmt.pdb -o mmt_box.gro editconf -f mmt_box.gro -o mmt_newbox.gro -box 5.800 5.811 7.5 -center 2.499 2.658 0.647 genbox -cp pla.gro -o pla_box.gro editconf -f pla_box.gro -o pla_newbox.gro -box 5.800 5.811 7.5 -center 2.732 2.722 4.277 genbox -cp mmt_newbox.gro -ci pla_newbox.gro -nmol 1 -o mmt_pla.gro -try 100 Image of composite box: http://s24.postimg.org/w9g7w6zwl/MMT_PLA.png After this I run the energy minimization using following commands grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 1 mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log -nt 1 The structure after energy minimization: http://s24.postimg.org/3l39syxqd/After_EM.png Below are the links for em.mdp, and system.top em.mdp : http://pastebin.com/3YsPR4FX system.top : http://pastebin.com/2PXdPA9P I hope this is everything you require. Thanks for you help. -- Message: 3 Date: Thu, 04 Apr 2013 04:14:57 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Applying periodic boundary conditions in energy minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 515d3681.30...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/3/13 9:46 PM, Abhinav Agrawal wrote: Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz This last line means PBC are being applied. Your observations are consistent with using a box that is too small for the solute, but since you haven't supplied information as to (1) what the system is, (2) how you built it, or (3) how large the box is, there's very little to say beyond speculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin I am using a composite system of polymer and clay. The composite box (5.8 nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm * 5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox. Should I increase the size of the composite box. Also, If I increase the size of the box how do I ensure that the density of the system does not chance. Thanks for your help. No, the box size seems reasonable. I only suggested that because the behavior you described (unfolding of the polymer) seemed to indicate spurious forces across PBC. As Tsjerk rightly noted, there's no such thing as outside of an infinite system. Without the exact sequence of commands and links to before and after images of the behavior you're seeing, there's not really much anyone can do to help. -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] Applying periodic boundary conditions in energy minimization
Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz I used the following commands: grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2 mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log Can you please tell me what I am doing wrong. Thanks in advance -- 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] Using two integrators in energy minimization
I want to use both steepest descent and conjugate gradient in my energy minimization. I need the system to use steepest descent for a given number of steps and then switch over to conjugate gradient. Can anyone please suggest how I can do this? How should I make the em.mdp file Thanks in advance. -- 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] Re: Applying periodic boundary conditions in energy minimization
Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz This last line means PBC are being applied. Your observations are consistent with using a box that is too small for the solute, but since you haven't supplied information as to (1) what the system is, (2) how you built it, or (3) how large the box is, there's very little to say beyond speculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin I am using a composite system of polymer and clay. The composite box (5.8 nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm * 5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox. Should I increase the size of the composite box. Also, If I increase the size of the box how do I ensure that the density of the system does not chance. Thanks for your help. -- 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] Making composite box in gromacs
I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. Thanks in advance. -- 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] Re: gmx-users Digest, Vol 107, Issue 133
Actually my doubt was how to make a simulation box from two structure files i.e. how do i keep the clay and poymer boxes close to each other to run energy minimization Message: 4 Date: Sun, 31 Mar 2013 07:38:38 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Making composite box in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5158203e.3020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/31/13 6:38 AM, Abhinav Agrawal wrote: I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. The concepts of top and bottom are irrelevant in a periodic system. You can position anything within the unit cell wherever you like with editconf -center. -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
