[gmx-users] Error in MD

[Mark Abraham]

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 :-)

Mark