[gmx-users] Error in MD

Dhananjay joshi joshidc_in1 at rediffmail.com
Tue Dec 13 13:11:49 CET 2005

Yes Mark,

You are right.

using "gmx_dump -s CORE_MTB_em.tpr | less" i found large vector of velocities (v) after the large vector of positions (x) and that they are all non-zero.

what should I do now ?

Should I go through all the steps again which I have shown to you or any other suggestion ?

Because of short of time,I have to stop here today. But I am waiting for your reply. I will act on it tomorrow only...

Thanks again..


On Tue, 13 Dec 2005 Mark Abraham wrote :
>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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