[Fwd: Re: Re: [gmx-users] Error in MD]

Mark Abraham Mark.Abraham at anu.edu.au
Tue Dec 13 11:33:56 CET 2005

-------- Original Message --------
Subject: Re: Re: [gmx-users] Error in MD
Date: Tue, 13 Dec 2005 09:16:19 +0000
From: Dhananjay joshi <joshidc_in1 at rediffmail.com>
Reply-To: Dhananjay joshi <joshidc_in1 at rediffmail.com>
To: Mark Abraham <Mark.Abraham at anu.edu.au>

   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....


On Tue, 13 Dec 2005 Mark Abraham wrote :
>Dhananjay chandrashekhar joshi wrote:
>>   I am beiginer in the field of MD. I was trying MD and I got following fatal error. 
>>There can be a number of reasons for the large velocities in your system. If it happens at the beginning of the simulation, your system might be not equilibrated well enough (e.g. it contains some bad contacts). Try a(nother) round of energy minimization to fix this. 
>>The I have agin tried EM. But it id of no use...
>In what way...?
>You will need to describe what you are doing in more detail. How are you generating your velocities?

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