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?
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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--
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________________________________________________________________________
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
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