[gmx-users] making a box of water

[Payman Pirzadeh]

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?

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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