Re: [gmx-users] free energy perturbations and B-parameter specifications
Hi
You have to be more specific...
Did you just do one sim for Gly->Ala?
Are you sure, you did the simulations in a way, you can compare it to
exp. results? (think about doing the perturbation once in water and once
in vacuum or so)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Soren Enemark wrote:
Dear Gromacsers,
I have been doing free energy perturbations Gly->Ala in one strand of
collagene.
Now, the problem is that I have later closely reread the section 5.6.4
("Free
Energy Calculations") p. 105 in which it says:
"Bonded interactions between atoms that are not perturbed do not need B
parameter specifications ..".
My questions are:
1. Does this mean that bonded interactions between atoms that ARE
perturbed DO need B parameter specifications? Even if they are the same
in state
A and B?
2. What about the other topology parameters (angles, dihedrals etc), do
they need to be specified too?
3. What happens if I have not specified these specifications?
The relevant parts of the topology file which I use are:
[ atoms ]
87 N 13ALA N 49 -0.2814.0067 ;
qtot 0.72
88 H 13ALA H 49 0.28 1.008 ;
qtot 1
89CH2 13ALA CA 50 0 14.027
CH1 0.0 3.019 ; qtot 1
90DUM 13ALA CB 50 0 15.035
CH3 0.0 15.035 ; qtot 1
91 C 13ALA C 51 0.38 12.011 ;
qtot 1.38
92 O 13ALA O 51 -0.3815.9994 ;
qtot 1
...
[ bonds ]
...
8789 2gb_20
8990 2gb_26
8991 2gb_26
...
[ angles ]
858789 2ga_30
888789 2ga_17
878990 2ga_12
878991 2ga_12
908991 2ga_12
899192 2ga_29
899193 2ga_18
And so on, ie, no B specifications have been done except for the atoms!
Best regards, and thank you in anticipation,
Soren
Ps. One (non-gromacs -sorry) question, given that the above is not wrong:
For the pertubation Gly->Ala I have get a deltaG of 0.8 kcal/mol.
Looking through literature, this does not seem all wrong, say if the
pertubation took place in an alpha-helix. On the other hand, it is
close to the thermal energy (~kT), and a previous article doing the
exact same perturbation arrives at a deltaG around 8.6 kcal/mol. Could
anyone comment on that?
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Re: [gmx-users] free energy perturbations and B-parameter specifications
On Jul 17, 2007, at 4:45 PM, Soren Enemark wrote:
Dear Gromacsers,
I have been doing free energy perturbations Gly->Ala in one strand
of collagene.
Now, the problem is that I have later closely reread the section
5.6.4 ("Free
Energy Calculations") p. 105 in which it says:
"Bonded interactions between atoms that are not perturbed do not
need B parameter specifications ..".
My questions are:
1. Does this mean that bonded interactions between atoms that ARE
perturbed DO need B parameter specifications? Even if they are the
same in state
A and B?
2. What about the other topology parameters (angles, dihedrals
etc), do they need to be specified too?
3. What happens if I have not specified these specifications?
Since a couple of years we automatically copy the A state parameters
to the B state if the latter aren't specified.
So, there are really three options e.g. for an entry in the [ bonds ]
section:
1. You only specify the bond atoms & type without any parameters
(most common approach)
In this case, the A state parameters will be assigned based on
the atomtypes in the A state, and the B state parameters likewise
based on the B state atomtypes.
The interaction is perturbed.
2. You provide the A state parameters explicitly, but not any B state
parameters:
Since you've decided to override the automatic assignment your
choice will be used in both the A and B states (i.e., the interaction
will not be perturbed)
3. You provide both A and B state parameters explicitly:
Your parameters will be assigned to each state, and the
interaction is perturbed.
Cheers,
Erik
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[gmx-users] free energy perturbations and B-parameter specifications
Dear Gromacsers,
I have been doing free energy perturbations Gly->Ala in one strand of
collagene.
Now, the problem is that I have later closely reread the section 5.6.4 ("Free
Energy Calculations") p. 105 in which it says:
"Bonded interactions between atoms that are not perturbed do not need B
parameter specifications ..".
My questions are:
1. Does this mean that bonded interactions between atoms that ARE perturbed
DO need B parameter specifications? Even if they are the same in state
A and B?
2. What about the other topology parameters (angles, dihedrals etc), do they
need to be specified too?
3. What happens if I have not specified these specifications?
The relevant parts of the topology file which I use are:
[ atoms ]
87 N 13ALA N 49 -0.2814.0067 ; qtot
0.72
88 H 13ALA H 49 0.28 1.008 ; qtot 1
89CH2 13ALA CA 50 0 14.027 CH1 0.0
3.019 ; qtot 1
90DUM 13ALA CB 50 0 15.035 CH3 0.0
15.035 ; qtot 1
91 C 13ALA C 51 0.38 12.011 ; qtot
1.38
92 O 13ALA O 51 -0.3815.9994 ; qtot 1
...
[ bonds ]
...
8789 2gb_20
8990 2gb_26
8991 2gb_26
...
[ angles ]
858789 2ga_30
888789 2ga_17
878990 2ga_12
878991 2ga_12
908991 2ga_12
899192 2ga_29
899193 2ga_18
And so on, ie, no B specifications have been done except for the atoms!
Best regards, and thank you in anticipation,
Soren
Ps. One (non-gromacs -sorry) question, given that the above is not wrong:
For the pertubation Gly->Ala I have get a deltaG of 0.8 kcal/mol. Looking
through literature, this does not seem all wrong, say if the pertubation took
place in an alpha-helix. On the other hand, it is close to the thermal energy
(~kT), and a previous article doing the exact same perturbation arrives at a
deltaG around 8.6 kcal/mol. Could anyone comment on that?
-
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