[gmx-users] Energy of a box of water
Payman Pirzadeh
ppirzade at ucalgary.ca
Wed Jul 15 22:45:49 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 2:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
> -----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.
Then it is fine. Which energy do you get for your own model?
These are the results I got. It includes all the initial equilibration time
during which simulation box got distorted.
Energy Average RMSD Fluct. Drift Tot-Drift
----------------------------------------------------------------------------
---
Potential -21955.7 739.133 538.245 -1.7548 -1754.8
Kinetic 4015.45 105.699 98.5134 -0.132693 -132.693
Total -17940.3 775.785 552.229 -1.88749 -1887.49
If I ignore that piece of trajectory, then the average will be 22174.95.
But, I can not understand how these values are fine? What is the connection
between the values in the tables and the literature values (~-40kJ/mol)? I
am truly confused!!!
>
>
>
>
>
>
>> 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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>>>>> posting!
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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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