[gmx-users] get 3 roation angles over time

Dear Gromacs users, my system consists of two rigid bodies "a" and "b". The body "a" has no rotation or translation over time. Body "b" rotates and translates over time. For my system I got the initial structure as PDB file and a XTC trajectory. How do I get in any easy way from the XTC trajector

Re: [gmx-users] get 3 roation angles over time

Hi Marc, Which rotation angles? I suppose you mean the Euler angles, but then, XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're interested. Cheers, Tsjerk On Fri, Jan 1, 2010 at 9:02 AM, wrote: > Dear Gromacs users, > > my system consists of two rigid bodies "a" and "b". Th

[gmx-users] order parameter in the unsaturated lipid

Hi, I am working on protein membrane that the lipid have one the *unsaturated *bond on C9-C10.The force Field used is *united atom*. I have some questions. 1- Is Sc-c (order parameter) valid for this lipid that contains the unsaturated bond? 2- How to i calculate Sc-c ? 3- When i use g_order

Re: [gmx-users] order parameter in the unsaturated lipid

afsaneh maleki wrote: Hi, I am working on protein membrane that the lipid have one the _unsaturated _bond on C9-C10.The force Field used is _united atom_. I have some questions. 1- Is Sc-c (order parameter) valid for this lipid that contains the unsaturated bond? Please see the -unsat

[gmx-users] Position Restrain

Dear all, I am trying to put a chain of polyleucine in water - hexane interface. Now after putting the chain of the peptide there are some overlaps. To get rid of those overlaps I tried to run a MD with the position of polyleucine constant (or restrained). But during energy minimization the

Re: [gmx-users] Position Restrain

pandeyprithvi...@gmail.com wrote: Dear all, I am trying to put a chain of polyleucine in water - hexane interface. Now after putting the chain of the peptide there are some overlaps. To get rid of those overlaps I tried to run a MD with the position of polyleucine constant (or restrained). Bu

[gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visual

Re: [gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

Chih-Ying Lin wrote: Hi I used Gromacs version 3.3.3. OK, but unless you need scientific continuity with earlier work, use the much faster 4.0.7. Additionally, domain decomposition was not implemented before 4.0, so either you're mistaken about your subject line, or you're using a 4.0.x

Re: [gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

Hi Lin, > I used Gromacs version 3.3.3. There is no domain decomposition in gromacs 3.3.3. Furthermore, you again give no account of what you're doing in terms of command lines and don't show the grompp output. This is pointless. Tsjerk > My simulation system = one protein + 20 ligand + water

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

> > Hi > I used Gromacs version 3.3.3. > My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 > ) > MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total > After doing the energy minimization, => the potential energy is extremely > high ( say, ten to the 9th

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visua

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential e

Re: [gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Chih-Ying Lin wrote: Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy m

[gmx-users] Gromacs 3.3.3 => what MPI based on ?

Hi There is no domain decomposition with Gromacs 3.3.3. What MPI based on with Gromacs 3.3.3? Thank you Lin -- 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'

Re: [gmx-users] Gromacs 3.3.3 => what MPI based on ?

Chih-Ying Lin wrote: Hi There is no domain decomposition with Gromacs 3.3.3. What MPI based on with Gromacs 3.3.3? 3.x uses a particle-based decomposition. There's not much documentation of it. Basically the system gets sliced up spatially and distributed to the processes. You can get a v

Re: [gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Chih-Ying Lin wrote: Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy m

Re: [gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Mark Abraham wrote: Chih-Ying Lin wrote: Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total