[gmx-users] Energy of a box of water
Payman Pirzadeh
ppirzade at ucalgary.ca
Wed Jul 15 22:35:40 CEST 2009
-----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 2:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
> Hi,
> I tested TIP4P and SPC-E. I used the .gro files in /share/top of the
> gromacs. The outputs of energy are:
>
> TIP4P, 1ns npT, T=300K
>
> Energy Average RMSD Fluct. Drift
> Tot-Drift
>
----------------------------------------------------------------------------
> ---
> Potential -20929 115.164 113.745 0.0624384
> 62.4385
> Kinetic En. 3781.5 72.9061 72.4712 0.0275462
> 27.5462
> Total Energy -17147.5 98.1701 94.671 0.0899847
> 89.9848
> Temperature 299.906 5.78209 5.7476 0.00218465
> 2.18465
> Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000371707)
>
>
> SPC-E, npT, T= 300K
>
> Energy Average RMSD Fluct. Drift
> Tot-Drift
>
----------------------------------------------------------------------------
> ---
> Potential -24058.6 114.598 109.211 0.120286
> 120.287
> Kinetic En. 3848.77 73.862 73.7792 -0.0121097
> -12.1097
> Total Energy -20209.9 95.4042 90.1487 0.108177
> 108.177
>
> The potential energies are again half of what they should be! Exactly the
> same problem with my own six-site model. Initially I thought I might have
> done sth in my .itp file, but now, I really do not understand where the
> problem comes from!!!!
If these boxes contain 512 molecules that means the energy is -42 kJ/mol
for TIP4P and slightly lower for SPC/E. Exactly correct.
However the distribution contains boxes with 216 molecules, which makes
that this is way too low, it should be -9000 for TIP4P.
How many molecules do you have?
Based on the topology files, I have 515 molecules for SPCE and 506 for
TIP4P. have 515 molecules for SPCE and 506 for TIP4P.
>
> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>> ------------------------------------------------------------------------
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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