[gmx-users] using rerun to extract energies for protein fromtrr file

Siavoush Dastmalchi Dastmalchi.s at tbzmed.ac.ir
Wed Jan 14 10:31:29 CET 2009

Dear Mark,
Many thanks for your kind suggestion. I did all sorts of things as you suggested, however still I get the same error. Here are the commands that I use (I used grompp also to generate different tpr files):
$ tpbconv -s fullmd.tpr -n index.ndx -o tpxout.tpr
$ trjconv -f md_traj.trr -n index.ndx -s tpxout.tpr -o trajout.trr
$ mdrun_d -s tpxout.tpr -o md_prot_final.trr -c md_prot_final.gro -e md_prot.edr -g md_prot.log -rerun trajout.trr
I am a bit confused and don't know what I am doing wrong. Is there any way to extract coordinates of just protein molecule for different frames and then calculate their energies (this is just a guess)?
Cheers, Siavoush


From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Mon 2009/01/12 03:47 ب.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] using rerun to extract energies for protein fromtrr file

Siavoush Dastmalchi wrote:
> Dear list,
> I am trying to extract energy profile for a protein molecule using rerun program from trajectory obtained by MD of protein solvated in a water box. I have created index file and reedited the original mdp file (removed the SOLs from it) to get a new tpr file using grompp. I have extracted a coordinate file and also generated top file for this coordinate file. When I run the mdrun using -rerun option, it fails and gives the following error message:

tpbconv allows you to create subsets of .tpr files, so you should also
use trjconv to make a matching subset from your .trr files and then use
mdrun -rerun.

> ******************************
> Program mdrun_d, VERSION 3.3.1
> Source code file: clincs.c, line: 559
> Fatal error:
> Too many LINCS warnings (11741) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations.
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file, but normally it is better to fix the problem.
> ******************************

This does not look like you are doing a rerun. LINCS should not be
invoked, IMO.

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