Re: [gmx-users] Scripting Analysis tools in tcsh
On Fri, 30 Jun 2006, Arneh Babakhani wrote: > Hello GMX users, > > (this may be more of a tcsh question, but here goes anyway). > > I'm trying to write a script to go through some trajectories and > calculate hbonding. It looks like this: > > #!/bin/tcsh > foreach number (1 2 3 4 5 6 7 8 9 10 11) > g_hbond -f ../../FullMD/FullMD$number.trr -s > ../../FullMD/FullMD$number.tpr -num hbnum-all-$number <<+ > 1 > 12 > + > end You are probably having an extra space in front of the latter + sign. Now + and end are considered as input for g_hbond. Olli PS. For general shell script questions a newsgroup like comp.unix.shell is a good place to keep in mind. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] my protein gets cut while preparing for em
On Mon, 19 Jun 2006, Guillem Plasencia wrote: > Then i was curious and did trjconv my system (before running mdrun energy > minimization) into a pdb, and had a look at it, and i saw my protein was > splitted in three different molecules, one was inside the water box (but far > away from box center, lying in touch of one of the boxes' sides) and the > other two parts were completely outside the box. Worst of all, they were no > more one single peptidic chain, but separated one. I was having somewhat similar problem recently when I had multiple peptides in my system (I used genconf to generate them) but in the final structure they all had the same chain identifier, so pdb2gmx thought that I have only one long peptide in the system (with some 1 nm long bonds). If this is the reason, one way to check how many chains there are is to interactively choose termini groups with pdb2gmx, you should be prompted for each peptide unit. By the way, if it is somehow possible to tell genconf to generate repeated units with different chain identifiers, I would be interested to know. regards, Olli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] A problem with periodic boundary conditions
Hi all, While running an energy minimization with mdrun 3.3.1, I observed that different peptide units in the simulation box were translated in y direction out of the box, each by N*Ly, N=1,5 (N is peptide unit and Ly is the box y-dimension). The final structure (confout.gro) is a kind of staircase instead of beta sheet which I'm trying to simulate. Only one peptide and all solvent (water and Cl-) remain in the original box. This happens even after setting nsteps=1. My system is probably quite far from equilibrium but this kind of behaviour seems anyway unexpected. I used genconf to generate the initial structure (which looks fine) and it is these generated units which become translated with mdrun. Any suggestions how to solve this problem are welcome. best regards, Olli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
