[gmx-users] some prolem about genbox genconf and editconf

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 28 04:58:11 CET 2009

Dallas B. Warren wrote:
> How are you visualizing the system?  Using VMD?  In that case, bonds are 
> determined by how far apart the atoms are, it guesses what the bonding 
> is, since a .gro file (or a pdb) doesn’t have any bonding information in 
> it.  So what you are seeing is simply the fact you have scaled the box, 
> increasing or decreasing the distance between the atoms.  After a quick 
> EM the atoms will return to their correct spacing.

I haven't used this feature of editconf, but if the scaling is truly over
all coordinates, then Dallas's EM procedure will be necessary. It may also be
necessary to scale in smallish increments, lest the EM be poorly conditioned
with large forces.


> Dr. Dallas Warren
> Department of Pharmaceutical Biology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble 
> a nail.
> *From:* gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *DreamCatcher
> *Sent:* Wednesday, 28 October 2009 1:50 PM
> *To:* gmx-users at gromacs.org
> *Subject:* [gmx-users] some prolem about genbox genconf and editconf
> Hi everybody,
>      I have come across some problem when using genbox, genconf and 
> editconf try to make a box with a certain density and a certain number 
> of polymer chains.
> First, I use genbox to have one polymer chain filled in the box without 
> any solvent.Then I use genconf to pile up 27 polymer chains ,after that 
> I use editconf to designate a density of  0.3 g/ml to attain the final 
> goal. When I finish it, i find that all the bond that connect the atoms 
> are gone and all the atoms disperse in the box.
>     In another try, I first use a pdb file which contains only one 
> polymer chain to genconf a box with 27polymer chain, and then use 
> editconf to designate the density, but finally I get a box with lots of 
> bonds that might not present in a normal structure, like a carbon was 
> bonded with a 3 or 4 or even more atoms distance long and the bonds 
> connect with it is overcount. What is the prolem? How can I fix it? 
> Thanks in advance,
> Celeste
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