[gmx-users] Energy of a box of water
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 15 22:49:31 CEST 2009
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 2:38 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!!!
You have to divide by the number of molecules.
g_energy -nmol N
>
>
>
>>
>>
>>
>>
>>
>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>> ------------------------------------------------------------------------
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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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