[gmx-users] genconf

[Justin A. Lemkul]

Payman Pirzadeh wrote:
> Hi Justin,
> I checked the trjconv help. It also takes .gro files. If so, do I still need
> to provide a .tpr file? (if yes, then the output can be .gro?)
> 

Any of the listed file formats can be input or output.  To fix "broken" 
molecules, you must supply a .tpr file.  If you run trjconv without it, you will 
get an error.

-Justin

> Payman
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Justin A. Lemkul
> Sent: July 22, 2009 6:01 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] genconf
> 
> 
> 
> 
> 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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 

-- 
========================================

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

========================================