[gmx-users] genconf

[Justin A. Lemkul]

Payman Pirzadeh wrote:
> Hello,
> I minimized the initial output (from another simulation) first; then I
> replicated it. This time, the minimization of the bigger box was done more
> easily! I ran an MD simulation with the bigger box and after 6 hours, it has
> not crashed yet.
> But, I have a question. When we replicate a box, and in the primary box one
> molecule is dissected into pieces due to pbc, will GROMACS return the
> molecules to its original shape during MD run or not?

No, it does not.

> I believe, without minimization, these dissected pieces will remain in the
> middle of the box and interfere with their replicated versions. Maybe,
> 'genconf' should be modified for such replications to maintain the pbc
> between the new molecules at the boundaries and fix the problem with the
> particle in the middle of the new bigger box!
> 

It can easily be accomplished using a .tpr file, and by using trjconv -pbc 
whole.  After molecules are whole, then use genconf.

-Justin

> Payman 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Payman Pirzadeh
> Sent: July 22, 2009 9:22 AM
> To: 'Discussion list for GROMACS users'
> Subject: RE: [gmx-users] genconf
> 
> Thanks a lot Mark! I will run the system for equilibration and then try to
> replicate it. I will keep you guys posted.
> 
> Payman
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Mark Abraham
> Sent: July 21, 2009 11:01 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] genconf
> 
> Payman Pirzadeh wrote:
>> Yes and no!
>> Sometimes there is an overlap, but sometimes I could find nothing! In the
>> simplest case, how can we avoid overlaps in a way that the crystal
> structure
>> is maintained under pbc?
>> Can the option "-dist" help here?
> 
> Replicating a box that was not designed for periodicity will always have 
> this problem. Whether the box is too small or two large, there will 
> either be steric clashes, or vacuums that will need filling. The general 
> solution is to equilibrate your box under PBC prior to replication. Now 
> the box size and the atomic spacings will be plausible, and the 
> replication will not of necessity introduce artifacts.
> 
> Mark
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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