Hi all, I am using gromacs to simulate the course grain for DNA. it is called the super-atoms including Phosphate (P),Sugar(S),Adenine base(Ab),Thymine(Tb). I have defined them in the .atp file like this, Ab 134.1; Adenine base Tb 125.1; Thymine base S 83.11; Sugar P 94.97; Phosphate But when I run this , it always shows that the atomtype "Ab" not found and Twin-range neighbour searching (NS) with simple NS algorithm not implemented .
I wonder whether anyone of us can tell me how to slove this problems. In addition , I wonder how I can define the potential which is not included in the gromacs. Thank you for any suggestion. Regards, Yang He ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Yang Ye [EMAIL PROTECTED] Sent: Monday, October 13, 2008 7:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Selecting part of the trajectory Hi, This is a common problem to long trajectory. It is fine as long as there is no real corruption in the trajectory file, caused by network, disk, etc. Solution: Shift a bit backward from the -b, this may be a few hundred ps or several ns, then extract the segment you would like to have from this secondary trajectory. Regards, Yang Ye ----- Original Message ---- From: #NGUYEN CONG TRI# <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Monday, October 13, 2008 3:47:32 PM Subject: [gmx-users] Selecting part of the trajectory Hi all, I want get the snapshots every 5ps of the last 1ns in a 20 ns simulation. So I want to cut out the last 1ns. I was able to do that using -b and -e flags of trjconv, say -b 19000 and -e 20000 for a .trr trajectory. However, to save disk space I converted it into .xtc format and I cannot use trjconv with -b and -e flags anymore. I got error msg like: Fatal error: Specified frame doesn't exist or file not seekable One more thing, my system consists of a protein and a ligand. At some snapshots, the ligand just jumps out of the box even when I used -pbc mol -ur compact. I tried with -pbc nojump and other option as well but none works perfectly in all cases. How to make sure that the ligand always stays with the protein so that I can write the script to automatically generate the snapshots and do some post-processing on them. Thank you for any suggestion. Regards, Tri _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
