Payman Pirzadeh wrote:
-----Original Message-----
From: [email protected] [mailto:[email protected]]
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: [email protected] [mailto:[email protected]]
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: [email protected]
[mailto:[email protected]]
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: [email protected]
[mailto:[email protected]]
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: [email protected]
[mailto:[email protected]]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 10:14 AM
To: [email protected]; '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: [email protected]
[mailto:[email protected]]
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: [email protected]
[mailto:[email protected]]
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: [email protected]
[mailto:[email protected]]
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
[email protected] [email protected] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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