Re: [gmx-users] -pbc nojump

Thank you very much from your reply. Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Thursday, December 29, 2011 1:56 AM Subject: Re: [gmx-users] -pbc nojump Hi Sara, Please keep discussions on the

Re: [gmx-users] -pbc nojump

Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. > 1- trjconv -f md.trr -o md1.xtc -n i

Re: [gmx-users] -pbc nojump

Hi Sara, The problem is that your micelle is formed at the end of the trajectory. To get what you want, you need to mirror the trajectory, follow the procedure you followed, and mirror the resulting trajectory. I posted a piece of python code for mirroring a trajectory a while back: http://lists.g

[gmx-users] -pbc nojump

Dear GROMACS users, I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of my simulation. For analysis I should do three steps for micelle clustering at http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering  Steps 1 and 2 work good and

Re: [gmx-users] -pbc nojump

On 20/10/2010 10:26 PM, shahab shariati wrote: Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? Anything that measures where something is relative to another. Normal

[gmx-users] -pbc nojump

Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search th

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:55 PM, leila karami wrote: Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what i

[gmx-users] -pbc nojump

Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what is your mean of [You might need two passes with

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:24 PM, leila karami wrote: Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. What is the problem? :-) You might need two passes with trjconv. Mark -- gmx-users mailing

[gmx-users] -pbc nojump

Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:07 PM, leila karami wrote: Hi gromacs users I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By this

[gmx-users] -pbc nojump

Hi gromacs users I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By this way my first problem is solved. 1) Should I