[gmx-users] making a box of water

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 16 20:08:29 CEST 2009 


Payman Pirzadeh wrote:
> But, I am using a .pdb file as the input of the gromacs. Does the
> preparation of pdb file differ from software to software?
> 

It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a 
.pdb file (I always use .gro).  What you can try to do is transform your .pdb 
into .gro format with editconf, and read the last line of the .gro file.  That's 
any easy way to determine the size of the box Gromacs is finding.

-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 16, 2009 11:42 AM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] making a box of water
> 
> 
> 
> Payman Pirzadeh wrote:
>> Hello,
>> Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the
>> rvdw cutoff to 10A, but problem was still there.
>> Now I made my box bigger by using a visualization software. The new
>> dimensions are ~54*63*103.38(all in A). Again the same warning is given to
>> me about increasing the box size or reduce the rvdw.
>>
> 
> Well, Gromacs doesn't do anything in A, it's all nm, so be sure that
> everything 
> you're doing is consistent with Gromacs conventions.  There is no reason
> that 
> either of those boxe should be complaining about a 1.0-nm cutoff, so there
> has 
> to be something that messed up along the way.
> 
> -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 15, 2009 7:32 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] making a box of water
>>
>>
>>
>> Payman Pirzadeh wrote:
>>> Hello,
>>> I have an .pdb file from another simulation. I want to make the
>> appropriate
>>> input files to run a simulations. I have used grompp to produce the .tpr
>>> file, but I get the usual ERROR:
>>>
>>>  ERROR: The cut-off length is longer than half the shortest box vector or
>>> longer than the smallest box diagonal element. Increase the box size or
>>> decrease rvdw.
>>>
>>> I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still
>>> the problem persists! Smaller rvdw is not good for my system. Any
>>> suggestions?
>>>
>> Then you'll have to use a bigger box, most likely.  What is your smallest
>> box 
>> vector?  That should indicate the limits of your cutoffs.
>>
>> -Justin
>>
>>> Payman 
>>>
>>> -----Original Message-----
>>> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]
>>> On Behalf Of David van der Spoel
>>> Sent: July 15, 2009 12:23 PM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] making a box of water
>>>
>>> Payman Pirzadeh wrote:
>>>> Thanks Justin. 
>>>> Unfortunately, I realized that after I sent the e-mail. Anyways, I
>> started
>>>> running to models: SPCE and TIP4P to check the energies of these systems
>>> to
>>>> figure out where the problem with my own system (six-site model) could
>> be.
>>> I
>>>> will keep you posted. But, I have a question about the compressibility
>>>> factor used in .mdp file. Does that(if it is not a correct value) truly
>>>> affect the simulation when the reference pressure is set?
>>>>
>>> No, only the relaxation rate (with Berendsen scaling) resp. the 
>>> oscillation period with Parrinello Rahman.
>>>
>>>> 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 15, 2009 11:38 AM
>>>> To: Discussion list for GROMACS users
>>>> Subject: Re: [gmx-users] making a box of water
>>>>
>>>>
>>>>
>>>> Payman Pirzadeh wrote:
>>>>> Hi again,
>>>>> I have a question about the .itp files. When e.g. TIP4P.itp the
>> atomtypes
>>>> in
>>>>> the  [atoms ]are specifies as opls_???, doesn't grompp check the
>> database
>>>>> for the corresponding parameters? Or we should again manually specify
>> the
>>>> [
>>>>> atomtypes ] again in either .itp or .top file?
>>>>>
>>>> You need to #include "ffoplsaa.itp" to take care of everything related
> to
>>>> the 
>>>> OPLS-AA force field.  Invoking grompp is not magic, the topology has to
>>>> contain 
>>>> specific instructions for everything you need to handle in your system.
>>>>
>>>> -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 15, 2009 10:14 AM
>>>>> To: jalemkul at vt.edu; 'Discussion list for GROMACS users'
>>>>> Subject: RE: [gmx-users] making a box of water
>>>>>
>>>>> OK!
>>>>> I changed my .top file to 
>>>>>
>>>>> ;This is simulation for TIP4P water model
>>>>> [ defaults ]
>>>>> ; non-bondedtype        combrule        genpairs        FudgeLJ
>>>>> FudgeQQ         N
>>>>> 1                       2               NO
>>>>>
>>>>> ; include TIP4P topology
>>>>> #include "tip4p.itp"
>>>>>
>>>>> [ system ]
>>>>> Pure box of water
>>>>>
>>>>> [ molecules ]
>>>>> SOL               506
>>>>>
>>>>> But I still get the same error message! Should I include the [defaults]
>>> in
>>>>> the .itp file?
>>>>>
>>>>> 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 14, 2009 7:56 PM
>>>>> To: Gromacs Users' List
>>>>> Subject: Re: [gmx-users] making a box of water
>>>>>
>>>>>
>>>>>
>>>>> Payman Pirzadeh wrote:
>>>>>> Will #include "ffgmx.itp" solve my problem? Would it be a general
>>>> solution
>>>>>> or in each case I should specify (if I add other solutes such as
>>>>> proteins)?
>>>>>
>>>>> Well, ffgmx is deprecated, so it is probably not the best choice :)
>>>>> Choosing a 
>>>>> force field should not be a haphazard occasion, it is a very important
>>>>> choice. 
>>>>> For water models, parameters should be uniform, but if you're
> simulating
>>> a
>>>>> protein, you'll want to make a very educated decision.
>>>>>
>>>>> -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 14, 2009 7:07 PM
>>>>>> To: Gromacs Users' List
>>>>>> Subject: Re: [gmx-users] making a box of water
>>>>>>
>>>>>>
>>>>>> You need to #include an appropriate force field that contains the
>>>>>> [defaults], 
>>>>>> [atomtypes], etc. before you can define a [moleculetype].
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> Payman Pirzadeh wrote:
>>>>>>> Here is my .top file:
>>>>>>>
>>>>>>> ;This includes SPC-E potential
>>>>>>> #include "spce.itp"
>>>>>>>
>>>>>>> [ system ]
>>>>>>> Pure box of water
>>>>>>>
>>>>>>> [ molecules ]
>>>>>>> SOL             515
>>>>>>>
>>>>>>> I used the same thing with my own model, but it had worked.
>>>>>>>
>>>>>>> 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 14, 2009 6:54 PM
>>>>>>> To: Discussion list for GROMACS users
>>>>>>> Subject: Re: [gmx-users] making a box of water
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Payman Pirzadeh wrote:
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I am trying to make a box of water from three different water
> models.
>>> I
>>>>>>>> can make one from my own water model, but when I want to test TIP4P
>>> and
>>>>>>>> SPCE, as soon as it comes to energy minimization step and using
>>> grompp,
>>>>>>>> I get the following error message:
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Program grompp, VERSION 4.0.4
>>>>>>>>
>>>>>>>> Source code file: topio.c, line: 415
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Fatal error:
>>>>>>>>
>>>>>>>> Syntax error - File spce.itp, line 1
>>>>>>>>
>>>>>>>> Last line read:
>>>>>>>>
>>>>>>>> '[ moleculetype ]'
>>>>>>>>
>>>>>>>> Invalid order for directive moleculetype
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> What is the problem causing the code referring to itp file?
>>>>>>>>
>>>>>>> See the message I just sent.  Something is out of order in your .top
>>>>> file.
>>>>>>> -Justin
>>>>>>>
>>>>>>>> Regards,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Payman
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>> ------------------------------------------------------------------------
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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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