[gmx-users] making a box of water

[David van der Spoel]

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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> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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