[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: 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 > Subject: Re: [gmx-users] Re: Applying periodic boundary conditions in > energy minimization > To: Discussion list for GROMACS users > 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] 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" > Subject: Re:[gmx-users] Applying periodic boundary conditions in > energy minimization > To: "Discussion list for GROMACS users" > 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" 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: 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] 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] 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] 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 > Subject: Re: [gmx-users] Making composite box in gromacs > To: Discussion list for GROMACS users > 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
[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
