[gmx-users] making a box of water

Thu Jul 16 19:16:49 CEST 2009

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.

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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