[gmx-users] genconf

Wed Jul 22 04:04:40 CEST 2009

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?
> 

Maybe.  I've never had to use it.  I've replicated a few systems using genconf 
-nbox (water and lipids), but I've never encountered any problems.  In theory, 
PBC should be maintained since all genconf is doing is translating your system 
by a certain factor according to box dimensions.

-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 6:47 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

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