Re: [gmx-users] (no subject)

sarbani chattopadhyay wrote: hi, I want to extend my run, for which I will have to use 'tpbconv' command.But this time I want to change the frequencies in which the energies,velocities and 'xyz' coordinates will be written to the trajectory file. Is there any way to do it? Thanks in adv

Re: [gmx-users] gramicidin A

pragya chohan wrote: hi I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. D-amino acids are enantiomers of L-amino acids. Thus they're topologically identical. So you can use the same topology for them, unless your force field has an interaction that v

RE: [gmx-users] gramicidin A

> Date: Sat, 3 Nov 2007 19:23:32 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] gramicidin A>> pragya chohan wrote:>> hi>> I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids.>> D-a

Re: [gmx-users] gramicidin A

pragya chohan wrote: I had already read the refered pages . Great. I had made changes in the charge and improper dihedrals. Since you don't need to do this, it's best not to do this. But pdb2gmx doesnt seem to recognise those amino acids still. So your .rtp is broken somehow. Probably

[gmx-users] g_rdf problem

Dear all, I am having a problem in running some post analysis commands like g_rdf on my computer . When my simulation is complete I type in the following command to calculate the radial distribution function for the system " g_rdf -f traj.trr -s topol.tpr -o rdf.xvg -b 0 -e 20 " and the program g