[gmx-users] Error in MD
Mark.Abraham at anu.edu.au
Tue Dec 13 11:47:53 CET 2005
Dhananjay joshi wrote:
> Thanks for reply,
> Well let me again tell you that I am beginer in this field.
> I have chosen CORE_MTB.pdb file and performed following operations.
> 1. pdb2gmx -f CORE_MTB.pdb -o CORE_MTB.gro -p CORE_MTB.top
> 2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8
> 3. genbox -cp CORE_MTB.gro -cs -o CORE_MTB_b4em.gro -p CORE_MTB.top
> Then I have done energy minimization with following steps.
> 4. grompp -f em.mdp -po md_em.mdp -c CORE_MTB_b4em.gro -o CORE_MTB_em.tpr
> -p CORE_MTB.top
> 5. mdrun -s CORE_MTB_em.tpr -o CORE_MTB_em.trr -c CORE_MTB_b4pr.gro
> -e ener_b4pr.edr -g md_em.log
> and I got the error message..
> The velocities were define in .mdp files are as follows.
> ; Generate velocites is off at 300 K.
> gen_vel = no
> gen_temp = 300.0
> gen_seed = 173529
> I didn't understand what was wrong, I mean what are the things that I should take care of....
For an energy minimization you don't want any velocities - they're only
relevant for dynamics. Here, if everything has gone as you describe then
there won't be any velocities (yet) in the .tpr file. Try using
"gmx_dump -s CORE_MTB_em.tpr | less" and see if there is a large vector
of velocities (v) after the large vector of positions (x) and that they
are all zero. If they aren't, I suspect you haven't actually done as you
describe above. If they are all zero and mdrun is doing this, then I
don't know what is wrong.
Also, it's good netiquette to continue discussions that start on an
email list on that list, unless you are certain that it's of interest
only to the individual you're emailing. "Reply-all" is everyone's friend :-)
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