[gmx-users] Fwd: Residue 'COA' not found in residue topology

Hinge, Please keep discussions on the list, there may be others which have the same question. Also try to put some effort in writing a well readable e-mail. User list conversations are not school notes. In answer to your question... I'd start with a literature search. Plenty of people will have

Re: [gmx-users] Membrane protein simulation

Dear Yanzi,Dear users, Finally the genbox was run probably it was related to my gromacs compilation on red hat 5. But I have another question. After running simulation (the position-restrained molecular dynamics simulation) on the system including protein, pope, water and CL for 100 ps, the

Re: [gmx-users] pressure average in 3.3.1

Mark Abraham wrote: [EMAIL PROTECTED] wrote: Dear Gromacs-users, I have claculated pressures for a trajectory using g_energy. However, the average pressure that is calculated by the program automatically is quite different from the value I get when I average over the data in the output file

[gmx-users] problem installing gromacs

i was compling fftp3.1.2 using the cygwin...it was not sucessusful and giving a statement as... configure error : no acceptable ld found in $PATH please help me out thanking you abhishek ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] RMSD calculations by g_rms

Dear All, I have two queries regarding the rmsd calculations of gromacs run. 1. I was trying to calculate rmsd for 3ns run of my protein system. I did it in two ways: VMD (RMSD Traj tool) and g_rms. I found great differences in pattern. I know that VMD gives values in angstrom, instead g_rms

Re: [gmx-users] RMSD calculations by g_rms

On Mon, 31 Dec 2007 16:22:40 +0530 Monika Sharma [EMAIL PROTECTED] wrote: Dear All, I have two queries regarding the rmsd calculations of gromacs run. 1. I was trying to calculate rmsd for 3ns run of my protein system. I did it in two ways: VMD (RMSD Traj tool) and g_rms. I found great

[gmx-users] problem in pr.mdp file

hi gromacs users, iam getting problem while doing postion restrian for the protein system reunning very slow, but i have done md.mdp for another system( bilayer-popc) its running normally, whats the problem in my protein system? i have used pr.mdp file like i am enlosing along with my mail

Re: [gmx-users] problem in pr.mdp file

What's the difference between the two runs? Isolate which of the differences makes your simulation run slow, and then the answer might present itself. - Original Message From: sudheer [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Monday, December 31, 2007 12:20:48 PM Subject:

RE: [gmx-users] problem in bilayer simulation

I think you misunderstood my reply. I understood that it is a periodic boundry condition problem and used trjconv. But it writes a trajectory file. How do I make a gro file to input it into next run? I cant even use tpbconv command because trjconv writes a xtc file and I need a trr file for

Re: [gmx-users] problem in bilayer simulation

I'm going to assume you've read http://wiki.gromacs.org/index.php/Doing_Restarts. I suggest you also look more closely at the manual page for trjconv. - Original Message From: pragya chohan [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday,

[gmx-users] what is position restrain?

hi gmx users, i have one doubt regarding position restrain, if we want to do postion restrain in amber we mention the atoms in min.in and eq.in files of vaccum phase and in water phase but incase of gromacs where we will mention and more over when we will do postion restrain in gromacs. PR must

[gmx-users] problem in pr.mdp file

Thanks for response Mr.Alan Dodd 1) 1st run is simularion of position restrain of protein in water (25000 steps) - system running very very slow means for completion 10 steps it is taking more than 5 minutes or more 2) 2nd simulation is production step of popc in water (125000 steps ) - this

Re: [gmx-users] problem in pr.mdp file

I think it might be more illustrative to understand why you think two different systems will necessarily run at the same speed. How large is the protein/water system? If it is a billion atoms and you expect it to run as fast as a system containing only several thousand (running on the same

Re: [gmx-users] problem in pr.mdp file

What's the difference between the two runs? Isolate which of the differences makes your simulation run slow, and then the answer might present itself. Or use the compare-two-.tpr-files functionality of gmxcheck to see what the differences were, instead of the .mdp files which you might be

Re: [gmx-users] problem installing gromacs

i was compling fftp3.1.2 using the cygwin...it was not sucessusful and giving a statement as... configure error : no acceptable ld found in $PATH Probably you have a broken or incomplete Cygwin installation. Re-install it, and follow the instructions here

RE: [gmx-users] problem in bilayer simulation

I think you misunderstood my reply. I understood that it is a periodic boundry condition problem and used trjconv. But it writes a trajectory file. How do I make a gro file to input it into next run? Depending on what you're doing, you may not need one. See

Re: [gmx-users] what is position restrain?

hi gmx users, i have one doubt regarding position restrain, if we want to do postion restrain in amber we mention the atoms in min.in and eq.in files of vaccum phase and in water phase but incase of gromacs where we will mention and more over when we will do postion restrain in gromacs. PR

RE: [gmx-users] problem in bilayer simulation

I understood that it is a periodic boundry condition problem and used trjconv. But it writes a trajectory file. How do I make a gro file to input it into next run Thanks I guess I was wrong. trjconv does write gro files. In any case, working out how to do the restart is totally separate