[gmx-users] Re: Minimum distance periodic images, protein simulation

2013-09-21 Thread aksharma
Hi Justin, Thanks for your reply. I have some follow-up questions. Since the simulation is high temperature (450 K) there is slight unfolding of the protein. The box was set up as rhombic dodecahedron with 1.2 nm as the distance between solute and edge of box. pdb2gmx -f 1L2Y.pdb -o 1L2Y-proces

Re: [gmx-users] Re: Minimum distance periodic images, protein simulation

2013-09-21 Thread Mark Abraham
You can try a run in implicit solvent to get a feel for the maximum diameter of the protein while unfolding. You will not have any certainty unless you can afford a box whose diameter is that of the straight-line peptide... Mark On Sat, Sep 21, 2013 at 1:03 PM, aksharma wrote: > Hi Justin, > Tha

Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

2013-09-21 Thread James
Dear Mark and the rest of the Gromacs team, Thanks a lot for your response. I have been trying to isolate the problem and have also been in discussion with the support staff. They suggested it may be a bug in the gromacs code, and I have tried to isolate the problem more precisely. Considering th

Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

2013-09-21 Thread Mark Abraham
On Sat, Sep 21, 2013 at 2:45 PM, James wrote: > Dear Mark and the rest of the Gromacs team, > > Thanks a lot for your response. I have been trying to isolate the problem > and have also been in discussion with the support staff. They suggested it > may be a bug in the gromacs code, and I have trie

[gmx-users] Use of walls combining with the PME and pressure coupling

2013-09-21 Thread p . chunwang
  Dear all, I’m working on some simulations about the adsorption of protein on solid surfaces, which have slab geometry in the x-y plane. In order to reduce the amount of water molecules and at the same time to decrease the unphysical Coulomb interaction between periodic images in the z-direction,

[gmx-users] emstep unit

2013-09-21 Thread Atila Petrosian
Dear gromacs users What is the reason of this point that unit of the emstep (step size)is nm? I think ps (unit of time) is more resonable. If I am wrong, please give me explanation about this point. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] emstep unit

2013-09-21 Thread Justin Lemkul
On 9/21/13 1:47 PM, Atila Petrosian wrote: Dear gromacs users What is the reason of this point that unit of the emstep (step size)is nm? I think ps (unit of time) is more resonable. If I am wrong, please give me explanation about this point. Energy minimization is a non-dynamical process;

[gmx-users] emstep unit

2013-09-21 Thread Atila Petrosian
Dear Justin Thanks for your reply. Ok. You are right. There is no "time" during EM. For example, if I use nstep = 10,000 and emstep = 0.01, what means of Step size in this case, exactly? Please give me more explanation. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] No such moleculetype SOL

2013-09-21 Thread Jonathan Saboury
I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command "grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr" it e

Re: [gmx-users] No such moleculetype SOL

2013-09-21 Thread Mark Abraham
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury wrote: > I am doing this tutorial: > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html > > I have set up the randomly placed cyclohexane and water throughout the box. > The problem is when i try the command

[gmx-users] restarting the crashed run

2013-09-21 Thread Nidhi Katyal
Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file and finally running mdrun but with no cpi option 2) same as 1 but with -cpi option 3) using only mdrun comma

Re: [gmx-users] emstep unit

2013-09-21 Thread Justin Lemkul
On 9/21/13 2:47 PM, Atila Petrosian wrote: Dear Justin Thanks for your reply. Ok. You are right. There is no "time" during EM. For example, if I use nstep = 10,000 and emstep = 0.01, what means of Step size in this case, exactly? Please give me more explanation. A quick Google search tu

Re: [gmx-users] restarting the crashed run

2013-09-21 Thread Justin Lemkul
On 9/21/13 3:46 PM, Nidhi Katyal wrote: Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file Why would you run grompp? If you're using it as a source of coor

[gmx-users] Re: No such moleculetype SOL

2013-09-21 Thread Jonathan Saboury
>Have a look at how Justin's tutorial's .top gets access to a water topology. > >Mark Thank you very much for the response Mark! I've looked at his .top and it seems to me that how he included it is by adding "#include spc.itp". I've added that line to cyclohexane.top before and after the "#inclu

Re: [gmx-users] Re: No such moleculetype SOL

2013-09-21 Thread Justin Lemkul
On 9/21/13 5:15 PM, Jonathan Saboury wrote: Have a look at how Justin's tutorial's .top gets access to a water topology. Mark Thank you very much for the response Mark! I've looked at his .top and it seems to me that how he included it is by adding "#include spc.itp". I've added that line

[gmx-users] Confuse about trjconv tool

2013-09-21 Thread Caizk
Dear users, I was following Justin's tutorial and in the analysis step trjconv was used to account for any periodicity in the system and then analyses were conducted with the so-called "corrected" trajectory file. The first question is: does it means that particles might diffuse though one sid

Re: [gmx-users] Confuse about trjconv tool

2013-09-21 Thread Justin Lemkul
On 9/21/13 10:28 PM, Caizk wrote: Dear users, I was following Justin's tutorial and in the analysis step trjconv was used to account for any periodicity in the system and then analyses were conducted with the so-called "corrected" trajectory file. The first thing that is important to note

Re: [gmx-users] emstep unit

2013-09-21 Thread Tsjerk Wassenaar
It's the size of the attempted step in conformational space, the distance from one configuration to the next. Cheers, Tsjerk On Sep 21, 2013 10:11 PM, "Justin Lemkul" wrote: On 9/21/13 2:47 PM, Atila Petrosian wrote: > > Dear Justin > > Thanks for your reply. > > Ok. You ... A quick Google sea