[gmx-users] making a box of water

[Payman Pirzadeh]

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?

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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