[gmx-users] genconf

Wed Jul 22 03:48:53 CEST 2009

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?

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 21, 2009 6:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf

Payman Pirzadeh wrote:
> I am so sorry! I had sth in mind and I wrote sth else!!!
> My original box has zero charges and GROMACS shows no notes on this.
> As soon as the box is multiplies, then the note regarding the net charge
> shows up and causes the simulation to crash.
> 

Well, then, like I said, this is probably an accumulation of rounding
errors. 
It can probably be ignored.  The reason for the crash is more likely some
kind 
of atomic overlap generated by the use of genconf.

-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 21, 2009 6:25 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] genconf
> 
> 
> 
> Payman Pirzadeh wrote:
>> In my previous e-mail, I posted the amount of charge given by GROMACS:
>>
>>> NOTE 2 [file sixsitemodel.top, line 8]:
>>>
>>>   System has non-zero total charge: -1.220703e-04
>> Also, I run the system without multiplication, and it runs fine without
> any
>> notes on the presence of a net charge!!! But, as soon as it is
multiplied,
>> then it gives notes of net charge!
>>
> 
> Then I'm more confused (and hence why I asked the first time).  You said
> your 
> original system had a non-zero charge.  Now you say that there were no
notes
> 
> about net charge, so the original system was uncharged.
> 
> Depending on the size of your system, small rounding errors can accumulate
> and 
> cause tiny fractional charges.  I don't know if this is problematic or not
> (in 
> terms of the system charge that mdrun finds), but it could be why you are
> seeing 
> this note.
> 
> -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 21, 2009 6:13 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] genconf
>>
>>
>>
>> Payman Pirzadeh wrote:
>>> OK! Thanks for the tips on thermostat.
>>>
>>> I multiplied my .gro file by using the command "genconf". My original 
>>> box has non-zero charge, but the generated bigger box has some charges:
>>>
>>>  
>> Define "non-zero."  Is it at least an integer?  Should your system bet
net
> 
>> neutral at this stage in your system preparation?
>>
>> -Justin
>>
>>> NOTE 2 [file sixsitemodel.top, line 8]:
>>>
>>>   System has non-zero total charge: -1.220703e-04
>>>
>>>  
>>>
>>> Then, during minimization, the system experiences a large positive 
>>> potential and infinite force. Is there a technicality in using "genconf"

>>> that I am missing? Doesn't it read the dimensions of the box from .gro 
>>> file to make sure no particles are overlapping with the original box? Or

>>> no particle is coming from the new one in the old one?
>>>
>>>  
>>>
>>> Payman
>>>
>>>  
>>>
>>> *From:* gmx-users-bounces at gromacs.org 
>>> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Vitaly V. Chaban
>>> *Sent:* July 21, 2009 4:53 PM
>>> *To:* gmx-users at gromacs.org
>>> *Subject:* [gmx-users] Re: reliability of NOTES
>>>
>>>  
>>>
>>>
>>>     Hello,
>>>     I am trying to prepare the input files for an MD run. After running
>>>     grompp,
>>>     I received the following note:
>>>
>>>     NOTE 1 [file npt.mdp, line unknown]:
>>>      The Berendsen thermostat does not generate the correct kinetic
> energy
>>>      distribution. You might want to consider using the V-rescale
>>>     thermostat.
>>>
>>>     How reliable this note is?
>>>
>>>
>>> It's true.
>>>  
>>>
>>>     And how can I implement V-rescale thermostat in y
>>>     input file (I found nothing in the manual).
>>>
>>>
>>> Substitute "berendsen" with "V-rescale" in the mdp file.
>>>
>>>
>>>     Also, when I changed the thermostat to nose-hoover, it said that it
>>>     can not
>>>     be used with Berendsen barostat. Why?
>>>
>>> C'est la vie...
>>>
>>>
>>> -- 
>>> Vitaly V. Chaban, Ph.D. (ABD)
>>> School of Chemistry
>>> V.N. Karazin Kharkiv National University
>>> Svoboda sq.,4, Kharkiv 61077, Ukraine
>>> email: chaban at univer.kharkov.ua 
>>> <mailto:chaban at univer.kharkov.ua>,vvchaban at gmail.com 
>>> <mailto:vvchaban at gmail.com>
>>> skype: vvchaban, mob.: +38-097-8259698
>>> http://www-rmn.univer.kharkov.ua/chaban.html
>>> ===================================
>>> !!! Looking for a postdoctoral position !!!
>>> ===================================
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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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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